diff --git a/RUNS/JOB/map/intermediate_files.txt b/RUNS/JOB/map/intermediate_files.txt
index fca722a6b079b0580854c4e39bf94a73b43b5814..1b55da4cde67dcdf91ef4ad0287e56567676c6e9 100644
--- a/RUNS/JOB/map/intermediate_files.txt
+++ b/RUNS/JOB/map/intermediate_files.txt
@@ -1,25 +1,25 @@
-results/small_input/formatted.fasta
-results/small_input/header_sorted_catMappings.sam
-results/small_input/fa/reads.fa
-results/small_input/GenomeMappings.sam
-results/small_input/segemehlTranscriptome_map.sam
-results/small_input/noheader_GenomeMappings.sam
-results/small_input/oligoGenome_map.fa
-results/small_input/cutted.fasta
-results/small_input/segemehlGenome_map.sam
-results/small_input/oligoTranscriptome_converted.sam
-results/small_input/nhfiltered_GenomeMappings.sam
-results/small_input/oligoTranscriptome_map.fa
-results/small_input/oligoTranscriptome_report.txt
-results/small_input/TransToGen.sam
-results/small_input/concatenated_header_catMappings.sam
-results/small_input/oligoGenome_converted.sam
-results/small_input/TranscriptomeMappings.sam
-results/small_input/noheader_TranscriptomeMappings.sam
-results/small_input/oligoTranscriptome_sorted.fa
-results/small_input/collapsed.fasta
-results/small_input/catMappings.sam
-results/small_input/filtered_for_oligomap.fasta
-results/small_input/oligoGenome_sorted.fa
-results/small_input/nhfiltered_TranscriptomeMappings.sam
-results/small_input/oligoGenome_report.txt
\ No newline at end of file
+results/test_lib/formatted.fasta
+results/test_lib/header_sorted_catMappings.sam
+results/test_lib/fa/reads.fa
+results/test_lib/GenomeMappings.sam
+results/test_lib/segemehlTranscriptome_map.sam
+results/test_lib/noheader_GenomeMappings.sam
+results/test_lib/oligoGenome_map.fa
+results/test_lib/cutted.fasta
+results/test_lib/segemehlGenome_map.sam
+results/test_lib/oligoTranscriptome_converted.sam
+results/test_lib/nhfiltered_GenomeMappings.sam
+results/test_lib/oligoTranscriptome_map.fa
+results/test_lib/oligoTranscriptome_report.txt
+results/test_lib/TransToGen.sam
+results/test_lib/concatenated_header_catMappings.sam
+results/test_lib/oligoGenome_converted.sam
+results/test_lib/TranscriptomeMappings.sam
+results/test_lib/noheader_TranscriptomeMappings.sam
+results/test_lib/oligoTranscriptome_sorted.fa
+results/test_lib/collapsed.fasta
+results/test_lib/catMappings.sam
+results/test_lib/filtered_for_oligomap.fasta
+results/test_lib/oligoGenome_sorted.fa
+results/test_lib/nhfiltered_TranscriptomeMappings.sam
+results/test_lib/oligoGenome_report.txt
\ No newline at end of file
diff --git a/config/config.yaml b/config/config.yaml
index c7a3476f68a2d5baa06dbdc3fe5eea4be9f9a75b..25f1d33238d2113137a84775070b1ba2c7bc1759 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -24,20 +24,20 @@ bp_3p: [-1, 0, +1]
 
 #### PARAMETERS SPECIFIC TO INPUTS #####
 
-organism: "homo_sapiens/chrY"
+organism: "homo_sapiens/chr19" 
 
-homo_sapiens/chrY:
-  # URLs to genome, gene & miRNA annotations
-  genome_url: "ftp://ftp.ensembl.org/pub/release-98/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.Y.fa.gz"
-  gtf_url: "ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/Homo_sapiens.GRCh38.98.gtf.gz"
-  mirna_url: "https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3"
+homo_sapiens/chr19: # entry should match precisely what is in the "organism" section above omitting the ""
+  
+  # path to genome, gene & miRNA annotation files
+  genome_path: "test_files/homo_sapiens/chr19/Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz"
+  gtf_path: "test_files/homo_sapiens/chr19/Homo_sapiens.GRCh38.98.chr19.gtf.gz"
+  mirna_path: "test_files/homo_sapiens/chr19/hsa_chr19.gff3"
 
   # Chromosome name mappings between UCSC <-> Ensembl
-  # Other organisms available at: https://github.com/dpryan79/ChromosomeMappings
-  map_chr_url: "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt"
+  map_chr_path:  "test_files/homo_sapiens/chr19/GRCh38_UCSC2ensembl_chr19.txt"
   # Chromosome name mapping parameters:
-  column: 1
-  delimiter: "TAB"
+  column: 1 # Column number from input file where to change chromosome name
+  delimiter: "TAB" # Delimiter of the input file
 
 #######################################################################################################
 ####
@@ -48,13 +48,13 @@ homo_sapiens/chrY:
 #### PARAMETERS SPECIFIC TO INPUTS #####
 
 # All of these are produced by the "prepare" workflow
-genome: "results/homo_sapiens/chrY/genome.processed.fa"
-gtf: "results/homo_sapiens/chrY/gene_annotations.filtered.gtf"
-transcriptome: "results/homo_sapiens/chrY/transcriptome_idtrim.fa"
-transcriptome_index_segemehl: "results/homo_sapiens/chrY/transcriptome_index_segemehl.idx"
-genome_index_segemehl: "results/homo_sapiens/chrY/genome_index_segemehl.idx"
-exons: "results/homo_sapiens/chrY/exons.bed"
-header_of_collapsed_fasta: "results/homo_sapiens/chrY/headerOfCollapsedFasta.sam"
+genome: "results/homo_sapiens/chr19/genome.processed.fa"
+gtf: "results/homo_sapiens/chr19/gene_annotations.filtered.gtf"
+transcriptome: "results/homo_sapiens/chr19/transcriptome_idtrim.fa"
+transcriptome_index_segemehl: "results/homo_sapiens/chr19/transcriptome_index_segemehl.idx"
+genome_index_segemehl: "results/homo_sapiens/chr19/genome_index_segemehl.idx"
+exons: "results/homo_sapiens/chr19/exons.bed"
+header_of_collapsed_fasta: "results/homo_sapiens/chr19/headerOfCollapsedFasta.sam"
 
 
 #### TOOL PARAMETERS #### 
@@ -86,6 +86,6 @@ mir_list: ["miRNA", "miRNA_primary_transcript"]
 
 # Resources: miR annotations, chromosome name mappings
 # All of these are produced by the "prepare" workflow
-mirnas_anno: "results/homo_sapiens/chrY/mirna_filtered.bed"
-isomirs_anno: "results/homo_sapiens/chrY/isomirs_annotation.bed"
+mirnas_anno: "results/homo_sapiens/chr19/mirna_filtered.bed"
+isomirs_anno: "results/homo_sapiens/chr19/isomirs_annotation.bed"
 ...
\ No newline at end of file
diff --git a/config/config_template.yaml b/config/config_template.yaml
index 62b061a4df558f67d29dad5a1a878d1dfa083456..3581c383e31f7e2f6fc2b04a98d55ab1ac566324 100644
--- a/config/config_template.yaml
+++ b/config/config_template.yaml
@@ -28,20 +28,21 @@ organism: "org/pre" # e.g., "homo_sapiens/GRCh38.100" or "mus_musculus/GRCm37.98
 # "pre" specifies the assembly version
 
 
-org/pre: # One section for each list item in "organism"; entry should match precisely what
-# is in the "organism" section above, one entry per list item above, omitting the ""
-  # URLs to genome, gene & miRNA annotations
-  genome_url: # FTP/HTTP URL to gzipped genome in FASTA format, Ensembl style
-  # e.g. "ftp://ftp.ensembl.org/pub/release-106/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz"
-  gtf_url: # FTP/HTTP URL to gzipped gene annotations in GTF format, Ensembl style
-  # e.g. "ftp://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.chr.gtf.gz"
-  mirna_url: # FTP/HTTP URL to unzipped microRNA annotations in GFF format, miRBase style
-  # e.g. "https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3"
+org/pre: # entry should match precisely what  is in the "organism" section above moitting the  ""
+
+  # path to genome, gene & miRNA annotation files
+  genome_path: # path to gzipped genome in FASTA format, Ensembl style
+  # e.g. "test_files/homo_sapiens/chr19/Homo_sapiens.GRCh38.dna_sm.chromosome.19.fa.gz"
+  gtf_path: # path to gzipped gene annotations in GTF format, Ensembl style
+  # e.g. "test_files/homo_sapiens/chr19/Homo_sapiens.GRCh38.98.chr19.gtf.gz"
+  mirna_path: # path to unzipped microRNA annotations in GFF format, miRBase style
+  # e.g. "test_files/homo_sapiens/chr19/hsa_chr19.gff3"
 
   # Chromosome name mappings between UCSC <-> Ensembl
   # Other organisms available at: https://github.com/dpryan79/ChromosomeMappings
-  map_chr_url: # FTP/HTTP URL to mapping table
-  # e.g. "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt"
+  map_chr_path: # path to mapping table
+  # e.g. "test_files/homo_sapiens/chr19/GRCh38_UCSC2ensembl_chr19.txt"
+  
   # Chromosome name mapping parameters:
   column: 1 # Column number from input file where to change chromosome name
   delimiter: "TAB" # Delimiter of the input file
diff --git a/scripts/filter_anno_gtf.sh b/scripts/filter_anno_gtf.sh
index df121c9588aafe69fd935cf17fb1b20c5f88212d..6cb67fac2bacf934c5d1999d2707626ffe2bbd7f 100755
--- a/scripts/filter_anno_gtf.sh
+++ b/scripts/filter_anno_gtf.sh
@@ -24,7 +24,6 @@ log_dir="$2"
 # Paths (DO NOT CHANGE!)  #Modified by Iborra P
 root="$PWD"
 resDir="${root}/${output_dir}"
-rawDir="${resDir}/raw"
 tmpDir="${root}/.tmp"
 logDir="${root}/${log_dir}"
 
@@ -35,8 +34,9 @@ logDir="${root}/${log_dir}"
 # files are concatenated after download
 # - It is assumed that the specified transcriptome files contain sequences for all transcripts in 
 # the (filtered) gene annotations
-geneAnnoURLs="$3"   #Modified by Iborra P
-
+geneAnnoRaw="$3"   #Modified by Iborra P
+geneAnno=${resDir}/gene_annotations.gtf.gz
+cp $geneAnnoRaw $geneAnno 
 # Filters
 # -------
 # - All filters are positive filters, i.e. entries meeting the specified filters are kept
@@ -65,7 +65,6 @@ set -o pipefail
 
 # Create directories
 mkdir --parents "$resDir"
-mkdir --parents "$rawDir"
 mkdir --parents "$tmpDir"
 
 # Create log file
@@ -78,20 +77,7 @@ rm -fr "$logFile"; touch "$logFile"
 ###  MAIN  ###
 ##############
 
-## GET & FILTER GENE ANNOTATIONS
-
-# Get gene annotation files
-echo "Downloading gene annotations..." >> "$logFile"
-for url in "${geneAnnoURLs[@]}"; do
-    wget "$url" --output-document "${rawDir}/$(basename "$url")" &> /dev/null
-done
-
-# Concatenate gene annotation files
-echo "Concatenating gene annotation files..." >> "$logFile"
-geneAnno="${resDir}/gene_annotations.gtf.gz"
-for url in "${geneAnnoURLs[@]}"; do
-    cat "${rawDir}/$(basename "$url")" >> "$geneAnno"
-done
+## FILTER GENE ANNOTATIONS
 
 # Filter gene annotations
 geneAnnoFilt="${resDir}/gene_annotations.filtered.gtf.gz"
@@ -146,7 +132,7 @@ rm "${resDir}/gene_annotations.gtf.gz"
 ###  END  ###
 #############
 
-echo "Original data in: $rawDir" >> "$logFile"
+echo "Original data: $geneAnno" >> "$logFile"
 echo "Processed data in: $resDir" >> "$logFile"
 echo "Done. No errors." >> "$logFile"
 >&2 echo "Done. No errors."
diff --git a/scripts/genome_process.sh b/scripts/genome_process.sh
index abc9d7fc1473c73bc993f4fa83eca93a624a9ecb..e9548528e0ddb2781bf898d3dc477c699d0c9e36 100755
--- a/scripts/genome_process.sh
+++ b/scripts/genome_process.sh
@@ -10,7 +10,7 @@
 ###  DESCRIPTION  ###
 #####################
 
-# Download and process genome sequences fasta files.
+# process genome sequences fasta files.
 
 ####################
 ###  PARAMETERS  ###
@@ -20,20 +20,17 @@
 output_dir="$1"
 log_dir="$2"   
 
-# # Paths (DO NOT CHANGE!)
-root="$PWD"
-#root="$(cd "$(dirname "$0" )" && pwd)"
+# Genome file
+# ----
+# It is assumed that the genome file 
+# contains only one chromosome
+genomeSeqFile="$3"   
 
+# Paths (DO NOT CHANGE!)
+root="$PWD"
 resDir="${root}/${output_dir}"
-rawDir="${resDir}/raw"
 logDir="${root}/${log_dir}"
 
-# URLs
-# ------
-# All URLs variables represent Bash arrays, so that multiple URLs can be provided; in that case, 
-# files are concatenated after download
-genomeSeqURLs="$3"   #Modified by Iborra P
-
 ########################
 ###  PRE-REQUISITES  ###
 ########################
@@ -45,7 +42,6 @@ set -o pipefail
 
 # Create directories
 mkdir --parents "$resDir"
-mkdir --parents "$rawDir"
 mkdir --parents "$logDir"
 
 # Create log file
@@ -57,23 +53,8 @@ rm -fr "$logFile"; touch "$logFile"
 ###  MAIN  ###
 ##############
 
-## GET & FILTER GENE ANNOTATIONS
-
-# Get genome sequences fasta files
-echo "Downloading genome sequences files..." >> "$logFile"
-# wget -i "${genomeSeqURLs}" --output-document "${rawDir}/${fileNamePrefix}.genome.fa.gz"
-# genomeSeq="${resDir}/${fileNamePrefix}.genome.fa.gz"
-
-for url in "${genomeSeqURLs[@]}"; do
-    wget "$url" --output-document "${rawDir}/$(basename "$url")" &> /dev/null
-done
-
-# Concatenate genome sequences fasta files
-echo "Concatenating genome sequences files..." >> "$logFile"
-genomeSeq="${resDir}/genome.fa.gz"
-for url in "${genomeSeqURLs[@]}"; do
-    cat "${rawDir}/$(basename "$url")" >> "$genomeSeq"
-done
+cp "${root}/${genomeSeqFile}" "${output_dir}/genome.fa.gz"
+genomeSeq="${output_dir}/genome.fa.gz"
 
 # Trim genome sequences IDs
 echo "Triming genome sequenes IDs..." >> "$logFile"
@@ -87,7 +68,7 @@ rm "${resDir}/genome.fa"
 ###  END  ###
 #############
 
-echo "Original data in: $rawDir" >> "$logFile"
+echo "Original data: ${root}/${genomeSeqFile}" >> "$logFile"
 echo "Processed data in: $resDir" >> "$logFile"
 echo "Done. No errors." >> "$logFile"
 >&2 echo "Done. No errors."
diff --git a/test/config.yaml b/test/config.yaml
index c5e23a221a244c731142db7fe29cb508cd75bbad..25f1d33238d2113137a84775070b1ba2c7bc1759 100644
--- a/test/config.yaml
+++ b/test/config.yaml
@@ -24,20 +24,20 @@ bp_3p: [-1, 0, +1]
 
 #### PARAMETERS SPECIFIC TO INPUTS #####
 
-organism: "homo_sapiens/chrY"
+organism: "homo_sapiens/chr19" 
 
-homo_sapiens/chrY:
-  # URLs to genome, gene & miRNA annotations
-  genome_url: "ftp://ftp.ensembl.org/pub/release-98/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.Y.fa.gz"
-  gtf_url: "ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/Homo_sapiens.GRCh38.98.gtf.gz"
-  mirna_url: "https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3"
+homo_sapiens/chr19: # entry should match precisely what is in the "organism" section above omitting the ""
+  
+  # path to genome, gene & miRNA annotation files
+  genome_path: "test_files/homo_sapiens/chr19/Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz"
+  gtf_path: "test_files/homo_sapiens/chr19/Homo_sapiens.GRCh38.98.chr19.gtf.gz"
+  mirna_path: "test_files/homo_sapiens/chr19/hsa_chr19.gff3"
 
   # Chromosome name mappings between UCSC <-> Ensembl
-  # Other organisms available at: https://github.com/dpryan79/ChromosomeMappings
-  map_chr_url: "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt"
+  map_chr_path:  "test_files/homo_sapiens/chr19/GRCh38_UCSC2ensembl_chr19.txt"
   # Chromosome name mapping parameters:
-  column: 1
-  delimiter: "TAB"
+  column: 1 # Column number from input file where to change chromosome name
+  delimiter: "TAB" # Delimiter of the input file
 
 #######################################################################################################
 ####
@@ -47,13 +47,14 @@ homo_sapiens/chrY:
 
 #### PARAMETERS SPECIFIC TO INPUTS #####
 
-genome: "results/homo_sapiens/chrY/genome.processed.fa"
-gtf: "results/homo_sapiens/chrY/gene_annotations.filtered.gtf"
-transcriptome: "results/homo_sapiens/chrY/transcriptome_idtrim.fa"
-transcriptome_index_segemehl: "results/homo_sapiens/chrY/transcriptome_index_segemehl.idx"
-genome_index_segemehl: "results/homo_sapiens/chrY/genome_index_segemehl.idx"
-exons: "results/homo_sapiens/chrY/exons.bed"
-header_of_collapsed_fasta: "results/homo_sapiens/chrY/headerOfCollapsedFasta.sam"
+# All of these are produced by the "prepare" workflow
+genome: "results/homo_sapiens/chr19/genome.processed.fa"
+gtf: "results/homo_sapiens/chr19/gene_annotations.filtered.gtf"
+transcriptome: "results/homo_sapiens/chr19/transcriptome_idtrim.fa"
+transcriptome_index_segemehl: "results/homo_sapiens/chr19/transcriptome_index_segemehl.idx"
+genome_index_segemehl: "results/homo_sapiens/chr19/genome_index_segemehl.idx"
+exons: "results/homo_sapiens/chr19/exons.bed"
+header_of_collapsed_fasta: "results/homo_sapiens/chr19/headerOfCollapsedFasta.sam"
 
 
 #### TOOL PARAMETERS #### 
@@ -85,6 +86,6 @@ mir_list: ["miRNA", "miRNA_primary_transcript"]
 
 # Resources: miR annotations, chromosome name mappings
 # All of these are produced by the "prepare" workflow
-mirnas_anno: "results/homo_sapiens/chrY/mirna_filtered.bed"
-isomirs_anno: "results/homo_sapiens/chrY/isomirs_annotation.bed"
+mirnas_anno: "results/homo_sapiens/chr19/mirna_filtered.bed"
+isomirs_anno: "results/homo_sapiens/chr19/isomirs_annotation.bed"
 ...
\ No newline at end of file
diff --git a/test/expected_output.md5 b/test/expected_output.md5
index 0d7c5c3444f559024b68f1b69d842b42d12e2ba7..456d9e137fffa126a770575a00992c385d55486e 100644
--- a/test/expected_output.md5
+++ b/test/expected_output.md5
@@ -1,74 +1,73 @@
-f37a213f94d11bf2260f50f2c9f199d2  results/homo_sapiens/chrY/genome.processed.fa.fai
-ce880d47bf97bb4c43589e51568d02d6  results/homo_sapiens/chrY/iso_anno_5p-1_3p-1.bed
-52114defcb2905049d1182d8e9458739  results/homo_sapiens/chrY/iso_anno_5p1_3p-1.bed
-a49b7296e91bf33ac560cb4dcaaf28f2  results/homo_sapiens/chrY/iso_anno_5p-1_3p0.bed
-583f395125f769102ff08ff84b60e0d3  results/homo_sapiens/chrY/genome.processed.fa
-a12a5577947ff6a3d6cd6c205a149b0b  results/homo_sapiens/chrY/iso_anno_rename_5p-1_3p-1.bed
-6fe52e2e126ef2e0c368fb1bf267f453  results/homo_sapiens/chrY/exons.gtf
-0b3dfe8cf4d644637671572fca629f69  results/homo_sapiens/chrY/gene_annotations.filtered.gtf
-40054d82cc01b4b44dbe476bdb50141c  results/homo_sapiens/chrY/headerOfCollapsedFasta.sam
-67e880cfae3cdfa5a17b5161106c7a05  results/homo_sapiens/chrY/iso_anno_rename_5p0_3p-1.bed
-548d8315be9dcfa394bfcb928e5a131c  results/homo_sapiens/chrY/iso_anno_rename_5p-1_3p0.bed
-221977ef10a502e764d9ff9a9e4d96cf  results/homo_sapiens/chrY/iso_anno_rename_5p-1_3p1.bed
-fc1068050ba1e7fa03e94087d9bd6978  results/homo_sapiens/chrY/iso_anno_5p0_3p0.bed
-c27229d158fdf70eb6f10313e988e9f7  results/homo_sapiens/chrY/iso_anno_5p0_3p-1.bed
-4fd9274d50a8dd7ce1533b03f2e538c0  results/homo_sapiens/chrY/iso_anno_5p1_3p0.bed
-dd6bc7e94c04f7a35c068335c9055b00  results/homo_sapiens/chrY/iso_anno_rename_5p0_3p1.bed
-bf1e37165b908729327599801ff5147b  results/homo_sapiens/chrY/transcriptome_idtrim.fa
-ba7404239073e3b67204af1803729884  results/homo_sapiens/chrY/mirna_chr_mapped.gff3
-11b0b7c50160aa8837dd92eda516c124  results/homo_sapiens/chrY/genome_index_segemehl.idx
-5ab1c2f39ab35fabc6673c73beb3097b  results/homo_sapiens/chrY/transcriptome.fa
-91e1facd80f93ef61f242050dd7d03c3  results/homo_sapiens/chrY/mirna_filtered.gff3
-e7e85f57e0476d1805c1cb64131dd75c  results/homo_sapiens/chrY/mirna_mature_filtered.bed
-8c6e976e926877f77946e9216db33a00  results/homo_sapiens/chrY/iso_anno_rename_5p0_3p0.bed
-a5a6fd2cab7d7919b80761fc25f2777a  results/homo_sapiens/chrY/transcriptome_index_segemehl.idx
-801dcc664f889e9148555dc85542402f  results/homo_sapiens/chrY/iso_anno_rename_5p1_3p-1.bed
-eb44404d89516497e6480d4dd33f2381  results/homo_sapiens/chrY/raw/Homo_sapiens.GRCh38.dna_sm.chromosome.Y.fa
-6bc49275f74ed1b43d80cf7598d387b9  results/homo_sapiens/chrY/raw/mirna.gff3
-d5eaafa9aec63e3fab632fc49392b54b  results/homo_sapiens/chrY/raw/Homo_sapiens.GRCh38.98.gtf
-8976aba06b980b721dbb4a9a4fd3509e  results/homo_sapiens/chrY/iso_anno_5p-1_3p1.bed
-79adc4c7382cf39b5f366e00a8696453  results/homo_sapiens/chrY/iso_anno_concat.bed
-909a2fc878c5ac0437344e4f5c6e58e3  results/homo_sapiens/chrY/isomirs_annotation.bed
-d2095c371c9b8b2c7cacd1024abf2d18  results/homo_sapiens/chrY/UCSC2ensembl.txt
-b23e51a933a2c453bd265ba60ef5442c  results/homo_sapiens/chrY/iso_anno_rename_5p1_3p1.bed
-51ac61c61825929f8f05c4b4f821f04d  results/homo_sapiens/chrY/exons.bed
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 d41d8cd98f00b204e9800998ecf8427e  results/test_lib/oligoTranscriptome_converted.sam
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 6c03db8848d24a36ad31879cadec7582  results/test_lib/formatted.fasta
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 d41d8cd98f00b204e9800998ecf8427e  results/test_lib/oligoTranscriptome_map.fa
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 d41d8cd98f00b204e9800998ecf8427e  results/test_lib/TransToGen.sam
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diff --git a/test/test_cleanup.sh b/test/test_cleanup.sh
index dd631ac2843af0972434d0521c857cb6df03ec3b..cb53ca3fffefd08ced1f5ce961473854723c63ac 100755
--- a/test/test_cleanup.sh
+++ b/test/test_cleanup.sh
@@ -21,6 +21,6 @@ rm -rf .snakemake/
 rm -rf .tmp/
 rm -rf logs/
 rm -rf results/
-rm -rf snakemake_report_*.html
+rm -rf snakemake_report*.html
 rm -rf wget-log*
 rm -rf .wget-hsts
diff --git a/test/test_files/homo_sapiens/chr19/GRCh38_UCSC2ensembl_chr19.txt b/test/test_files/homo_sapiens/chr19/GRCh38_UCSC2ensembl_chr19.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82b85829a9738e0e7240c3423260d8e2802bc72e
--- /dev/null
+++ b/test/test_files/homo_sapiens/chr19/GRCh38_UCSC2ensembl_chr19.txt
@@ -0,0 +1,44 @@
+chr19	19
+chr19_GL000209v2_alt	
+chr19_GL383573v1_alt	
+chr19_GL383574v1_alt	
+chr19_GL383575v2_alt	
+chr19_GL383576v1_alt	
+chr19_GL949746v1_alt	
+chr19_GL949747v2_alt	
+chr19_GL949748v2_alt	
+chr19_GL949749v2_alt	
+chr19_GL949750v2_alt	
+chr19_GL949751v2_alt	
+chr19_GL949752v1_alt	
+chr19_GL949753v2_alt	
+chr19_KI270865v1_alt	
+chr19_KI270866v1_alt	
+chr19_KI270867v1_alt	
+chr19_KI270868v1_alt	
+chr19_KI270882v1_alt	
+chr19_KI270883v1_alt	
+chr19_KI270884v1_alt	
+chr19_KI270885v1_alt	
+chr19_KI270886v1_alt	
+chr19_KI270887v1_alt	
+chr19_KI270888v1_alt	
+chr19_KI270889v1_alt	
+chr19_KI270890v1_alt	
+chr19_KI270891v1_alt	
+chr19_KI270914v1_alt	
+chr19_KI270915v1_alt	
+chr19_KI270916v1_alt	
+chr19_KI270917v1_alt	
+chr19_KI270918v1_alt	
+chr19_KI270919v1_alt	
+chr19_KI270920v1_alt	
+chr19_KI270921v1_alt	
+chr19_KI270922v1_alt	
+chr19_KI270923v1_alt	
+chr19_KI270929v1_alt	
+chr19_KI270930v1_alt	
+chr19_KI270931v1_alt	
+chr19_KI270932v1_alt	
+chr19_KI270933v1_alt	
+chr19_KI270938v1_alt	
diff --git a/test/test_files/homo_sapiens/chr19/Homo_sapiens.GRCh38.98.chr19.gtf.gz b/test/test_files/homo_sapiens/chr19/Homo_sapiens.GRCh38.98.chr19.gtf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..68a73e5dc34169c4951760e39dc773a3dc4d2222
Binary files /dev/null and b/test/test_files/homo_sapiens/chr19/Homo_sapiens.GRCh38.98.chr19.gtf.gz differ
diff --git a/test/test_files/homo_sapiens/chr19/Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz b/test/test_files/homo_sapiens/chr19/Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz
new file mode 100644
index 0000000000000000000000000000000000000000..aa9d9008fc9671ff3cf81535c68c1b4bd043ca35
Binary files /dev/null and b/test/test_files/homo_sapiens/chr19/Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz differ
diff --git a/test/test_files/homo_sapiens/chr19/hsa_chr19.gff3 b/test/test_files/homo_sapiens/chr19/hsa_chr19.gff3
new file mode 100644
index 0000000000000000000000000000000000000000..d185bd3e78e6418b7cabd5d36354a613a9472a2c
--- /dev/null
+++ b/test/test_files/homo_sapiens/chr19/hsa_chr19.gff3
@@ -0,0 +1,385 @@
+chr19	.	miRNA_primary_transcript	71973	72110	.	+	.	ID=MI0015980;Alias=MI0015980;Name=hsa-mir-1302-11
+chr19	.	miRNA	72045	72065	.	+	.	ID=MIMAT0005890_3;Alias=MIMAT0005890;Name=hsa-miR-1302;Derives_from=MI0015980
+chr19	.	miRNA_primary_transcript	804940	805001	.	+	.	ID=MI0017384;Alias=MI0017384;Name=hsa-mir-4745
+chr19	.	miRNA	804941	804963	.	+	.	ID=MIMAT0019878;Alias=MIMAT0019878;Name=hsa-miR-4745-5p;Derives_from=MI0017384
+chr19	.	miRNA	804977	804999	.	+	.	ID=MIMAT0019879;Alias=MIMAT0019879;Name=hsa-miR-4745-3p;Derives_from=MI0017384
+chr19	.	miRNA_primary_transcript	813584	813653	.	+	.	ID=MI0014231;Alias=MI0014231;Name=hsa-mir-3187
+chr19	.	miRNA	813627	813646	.	+	.	ID=MIMAT0015069;Alias=MIMAT0015069;Name=hsa-miR-3187-3p;Derives_from=MI0014231
+chr19	.	miRNA	813590	813612	.	+	.	ID=MIMAT0019216;Alias=MIMAT0019216;Name=hsa-miR-3187-5p;Derives_from=MI0014231
+chr19	.	miRNA_primary_transcript	1816159	1816238	.	-	.	ID=MI0008330;Alias=MI0008330;Name=hsa-mir-1909
+chr19	.	miRNA	1816203	1816223	.	-	.	ID=MIMAT0007882;Alias=MIMAT0007882;Name=hsa-miR-1909-5p;Derives_from=MI0008330
+chr19	.	miRNA	1816169	1816190	.	-	.	ID=MIMAT0007883;Alias=MIMAT0007883;Name=hsa-miR-1909-3p;Derives_from=MI0008330
+chr19	.	miRNA_primary_transcript	2234062	2234149	.	-	.	ID=MI0006316;Alias=MI0006316;Name=hsa-mir-1227
+chr19	.	miRNA	2234062	2234081	.	-	.	ID=MIMAT0005580;Alias=MIMAT0005580;Name=hsa-miR-1227-3p;Derives_from=MI0006316
+chr19	.	miRNA	2234133	2234149	.	-	.	ID=MIMAT0022941;Alias=MIMAT0022941;Name=hsa-miR-1227-5p;Derives_from=MI0006316
+chr19	.	miRNA_primary_transcript	2235829	2235926	.	-	.	ID=MI0022634;Alias=MI0022634;Name=hsa-mir-6789
+chr19	.	miRNA	2235899	2235922	.	-	.	ID=MIMAT0027478;Alias=MIMAT0027478;Name=hsa-miR-6789-5p;Derives_from=MI0022634
+chr19	.	miRNA	2235829	2235849	.	-	.	ID=MIMAT0027479;Alias=MIMAT0027479;Name=hsa-miR-6789-3p;Derives_from=MI0022634
+chr19	.	miRNA_primary_transcript	2250639	2250718	.	+	.	ID=MI0015852;Alias=MI0015852;Name=hsa-mir-4321
+chr19	.	miRNA	2250688	2250708	.	+	.	ID=MIMAT0016874;Alias=MIMAT0016874;Name=hsa-miR-4321;Derives_from=MI0015852
+chr19	.	miRNA_primary_transcript	2434914	2435000	.	-	.	ID=MI0022959;Alias=MI0022959;Name=hsa-mir-7108
+chr19	.	miRNA	2434980	2435000	.	-	.	ID=MIMAT0028113;Alias=MIMAT0028113;Name=hsa-miR-7108-5p;Derives_from=MI0022959
+chr19	.	miRNA	2434914	2434933	.	-	.	ID=MIMAT0028114;Alias=MIMAT0028114;Name=hsa-miR-7108-3p;Derives_from=MI0022959
+chr19	.	miRNA_primary_transcript	2630715	2630793	.	+	.	ID=MI0025520;Alias=MI0025520;Name=hsa-mir-7850
+chr19	.	miRNA	2630723	2630743	.	+	.	ID=MIMAT0030425;Alias=MIMAT0030425;Name=hsa-miR-7850-5p;Derives_from=MI0025520
+chr19	.	miRNA_primary_transcript	3961414	3961512	.	-	.	ID=MI0003652;Alias=MI0003652;Name=hsa-mir-637
+chr19	.	miRNA	3961429	3961452	.	-	.	ID=MIMAT0003307;Alias=MIMAT0003307;Name=hsa-miR-637;Derives_from=MI0003652
+chr19	.	miRNA_primary_transcript	4445978	4446048	.	+	.	ID=MI0017385;Alias=MI0017385;Name=hsa-mir-4746
+chr19	.	miRNA	4445987	4446009	.	+	.	ID=MIMAT0019880;Alias=MIMAT0019880;Name=hsa-miR-4746-5p;Derives_from=MI0017385
+chr19	.	miRNA	4446021	4446041	.	+	.	ID=MIMAT0019881;Alias=MIMAT0019881;Name=hsa-miR-4746-3p;Derives_from=MI0017385
+chr19	.	miRNA_primary_transcript	4770670	4770779	.	+	.	ID=MI0000265;Alias=MI0000265;Name=hsa-mir-7-3
+chr19	.	miRNA	4770700	4770723	.	+	.	ID=MIMAT0000252_1;Alias=MIMAT0000252;Name=hsa-miR-7-5p;Derives_from=MI0000265
+chr19	.	miRNA_primary_transcript	4932687	4932740	.	+	.	ID=MI0017386;Alias=MI0017386;Name=hsa-mir-4747
+chr19	.	miRNA	4932687	4932708	.	+	.	ID=MIMAT0019882;Alias=MIMAT0019882;Name=hsa-miR-4747-5p;Derives_from=MI0017386
+chr19	.	miRNA	4932719	4932740	.	+	.	ID=MIMAT0019883;Alias=MIMAT0019883;Name=hsa-miR-4747-3p;Derives_from=MI0017386
+chr19	.	miRNA_primary_transcript	6389638	6389703	.	-	.	ID=MI0022732;Alias=MI0022732;Name=hsa-mir-6885
+chr19	.	miRNA	6389674	6389698	.	-	.	ID=MIMAT0027670;Alias=MIMAT0027670;Name=hsa-miR-6885-5p;Derives_from=MI0022732
+chr19	.	miRNA	6389638	6389658	.	-	.	ID=MIMAT0027671;Alias=MIMAT0027671;Name=hsa-miR-6885-3p;Derives_from=MI0022732
+chr19	.	miRNA_primary_transcript	6392921	6392983	.	-	.	ID=MI0022635;Alias=MI0022635;Name=hsa-mir-6790
+chr19	.	miRNA	6392961	6392983	.	-	.	ID=MIMAT0027480;Alias=MIMAT0027480;Name=hsa-miR-6790-5p;Derives_from=MI0022635
+chr19	.	miRNA	6392925	6392945	.	-	.	ID=MIMAT0027481;Alias=MIMAT0027481;Name=hsa-miR-6790-3p;Derives_from=MI0022635
+chr19	.	miRNA_primary_transcript	6416410	6416511	.	-	.	ID=MI0016597;Alias=MI0016597;Name=hsa-mir-3940
+chr19	.	miRNA	6416434	6416455	.	-	.	ID=MIMAT0018356;Alias=MIMAT0018356;Name=hsa-miR-3940-3p;Derives_from=MI0016597
+chr19	.	miRNA	6416470	6416489	.	-	.	ID=MIMAT0019229;Alias=MIMAT0019229;Name=hsa-miR-3940-5p;Derives_from=MI0016597
+chr19	.	miRNA_primary_transcript	6736712	6736778	.	-	.	ID=MI0022636;Alias=MI0022636;Name=hsa-mir-6791
+chr19	.	miRNA	6736752	6736773	.	-	.	ID=MIMAT0027482;Alias=MIMAT0027482;Name=hsa-miR-6791-5p;Derives_from=MI0022636
+chr19	.	miRNA	6736712	6736732	.	-	.	ID=MIMAT0027483;Alias=MIMAT0027483;Name=hsa-miR-6791-3p;Derives_from=MI0022636
+chr19	.	miRNA_primary_transcript	7617439	7617505	.	+	.	ID=MI0022637;Alias=MI0022637;Name=hsa-mir-6792
+chr19	.	miRNA	7617439	7617459	.	+	.	ID=MIMAT0027484;Alias=MIMAT0027484;Name=hsa-miR-6792-5p;Derives_from=MI0022637
+chr19	.	miRNA	7617480	7617501	.	+	.	ID=MIMAT0027485;Alias=MIMAT0027485;Name=hsa-miR-6792-3p;Derives_from=MI0022637
+chr19	.	miRNA_primary_transcript	8389290	8389380	.	-	.	ID=MI0017865;Alias=MI0017865;Name=hsa-mir-4999
+chr19	.	miRNA	8389340	8389360	.	-	.	ID=MIMAT0021017;Alias=MIMAT0021017;Name=hsa-miR-4999-5p;Derives_from=MI0017865
+chr19	.	miRNA	8389311	8389330	.	-	.	ID=MIMAT0021018;Alias=MIMAT0021018;Name=hsa-miR-4999-3p;Derives_from=MI0017865
+chr19	.	miRNA_primary_transcript	10038354	10038413	.	+	.	ID=MI0019148;Alias=MI0019148;Name=hsa-mir-5589
+chr19	.	miRNA	10038354	10038374	.	+	.	ID=MIMAT0022297;Alias=MIMAT0022297;Name=hsa-miR-5589-5p;Derives_from=MI0019148
+chr19	.	miRNA	10038391	10038413	.	+	.	ID=MIMAT0022298;Alias=MIMAT0022298;Name=hsa-miR-5589-3p;Derives_from=MI0019148
+chr19	.	miRNA_primary_transcript	10230413	10230485	.	+	.	ID=MI0015851;Alias=MI0015851;Name=hsa-mir-4322
+chr19	.	miRNA	10230455	10230475	.	+	.	ID=MIMAT0016873;Alias=MIMAT0016873;Name=hsa-miR-4322;Derives_from=MI0015851
+chr19	.	miRNA_primary_transcript	10403458	10403538	.	-	.	ID=MI0006274;Alias=MI0006274;Name=hsa-mir-1181
+chr19	.	miRNA	10403505	10403525	.	-	.	ID=MIMAT0005826;Alias=MIMAT0005826;Name=hsa-miR-1181;Derives_from=MI0006274
+chr19	.	miRNA_primary_transcript	10552122	10552204	.	+	.	ID=MI0006328;Alias=MI0006328;Name=hsa-mir-1238
+chr19	.	miRNA	10552183	10552202	.	+	.	ID=MIMAT0005593;Alias=MIMAT0005593;Name=hsa-miR-1238-3p;Derives_from=MI0006328
+chr19	.	miRNA	10552122	10552144	.	+	.	ID=MIMAT0022947;Alias=MIMAT0022947;Name=hsa-miR-1238-5p;Derives_from=MI0006328
+chr19	.	miRNA_primary_transcript	10718404	10718503	.	+	.	ID=MI0003653;Alias=MI0003653;Name=hsa-mir-638
+chr19	.	miRNA	10718419	10718443	.	+	.	ID=MIMAT0003308;Alias=MIMAT0003308;Name=hsa-miR-638;Derives_from=MI0003653
+chr19	.	miRNA_primary_transcript	10780254	10780335	.	+	.	ID=MI0017387;Alias=MI0017387;Name=hsa-mir-4748
+chr19	.	miRNA	10780263	10780283	.	+	.	ID=MIMAT0019884;Alias=MIMAT0019884;Name=hsa-miR-4748;Derives_from=MI0017387
+chr19	.	miRNA_primary_transcript	10817426	10817496	.	-	.	ID=MI0000242;Alias=MI0000242;Name=hsa-mir-199a-1
+chr19	.	miRNA	10817469	10817491	.	-	.	ID=MIMAT0000231_1;Alias=MIMAT0000231;Name=hsa-miR-199a-5p;Derives_from=MI0000242
+chr19	.	miRNA	10817429	10817450	.	-	.	ID=MIMAT0000232_1;Alias=MIMAT0000232;Name=hsa-miR-199a-3p;Derives_from=MI0000242
+chr19	.	miRNA_primary_transcript	10828973	10829035	.	+	.	ID=MI0022638;Alias=MI0022638;Name=hsa-mir-6793
+chr19	.	miRNA	10828978	10828999	.	+	.	ID=MIMAT0027486;Alias=MIMAT0027486;Name=hsa-miR-6793-5p;Derives_from=MI0022638
+chr19	.	miRNA	10829016	10829035	.	+	.	ID=MIMAT0027487;Alias=MIMAT0027487;Name=hsa-miR-6793-3p;Derives_from=MI0022638
+chr19	.	miRNA_primary_transcript	11113474	11113534	.	+	.	ID=MI0022733;Alias=MI0022733;Name=hsa-mir-6886
+chr19	.	miRNA	11113479	11113499	.	+	.	ID=MIMAT0027672;Alias=MIMAT0027672;Name=hsa-miR-6886-5p;Derives_from=MI0022733
+chr19	.	miRNA	11113511	11113531	.	+	.	ID=MIMAT0027673;Alias=MIMAT0027673;Name=hsa-miR-6886-3p;Derives_from=MI0022733
+chr19	.	miRNA_primary_transcript	11495544	11495622	.	-	.	ID=MI0025750;Alias=MI0025750;Name=hsa-mir-7974
+chr19	.	miRNA	11495544	11495567	.	-	.	ID=MIMAT0031177;Alias=MIMAT0031177;Name=hsa-miR-7974;Derives_from=MI0025750
+chr19	.	miRNA_primary_transcript	12703601	12703664	.	-	.	ID=MI0033419;Alias=MI0033419;Name=hsa-mir-10395
+chr19	.	miRNA	12703647	12703664	.	-	.	ID=MIMAT0041621;Alias=MIMAT0041621;Name=hsa-miR-10395-5p;Derives_from=MI0033419
+chr19	.	miRNA	12703601	12703621	.	-	.	ID=MIMAT0041622;Alias=MIMAT0041622;Name=hsa-miR-10395-3p;Derives_from=MI0033419
+chr19	.	miRNA_primary_transcript	12787128	12787192	.	+	.	ID=MI0019285;Alias=MI0019285;Name=hsa-mir-5684
+chr19	.	miRNA	12787132	12787151	.	+	.	ID=MIMAT0022473;Alias=MIMAT0022473;Name=hsa-miR-5684;Derives_from=MI0019285
+chr19	.	miRNA_primary_transcript	12852260	12852327	.	+	.	ID=MI0022639;Alias=MI0022639;Name=hsa-mir-6794
+chr19	.	miRNA	12852265	12852284	.	+	.	ID=MIMAT0027488;Alias=MIMAT0027488;Name=hsa-miR-6794-5p;Derives_from=MI0022639
+chr19	.	miRNA	12852306	12852325	.	+	.	ID=MIMAT0027489;Alias=MIMAT0027489;Name=hsa-miR-6794-3p;Derives_from=MI0022639
+chr19	.	miRNA_primary_transcript	12920320	12920404	.	+	.	ID=MI0019302;Alias=MI0019302;Name=hsa-mir-5695
+chr19	.	miRNA	12920373	12920394	.	+	.	ID=MIMAT0022488;Alias=MIMAT0022488;Name=hsa-miR-5695;Derives_from=MI0019302
+chr19	.	miRNA_primary_transcript	12940484	12940540	.	+	.	ID=MI0022227;Alias=MI0022227;Name=hsa-mir-6515
+chr19	.	miRNA	12940486	12940506	.	+	.	ID=MIMAT0025486;Alias=MIMAT0025486;Name=hsa-miR-6515-5p;Derives_from=MI0022227
+chr19	.	miRNA	12940521	12940540	.	+	.	ID=MIMAT0025487;Alias=MIMAT0025487;Name=hsa-miR-6515-3p;Derives_from=MI0022227
+chr19	.	miRNA_primary_transcript	13836287	13836359	.	-	.	ID=MI0000081;Alias=MI0000081;Name=hsa-mir-24-2
+chr19	.	miRNA	13836289	13836310	.	-	.	ID=MIMAT0000080;Alias=MIMAT0000080;Name=hsa-miR-24-3p;Derives_from=MI0000081
+chr19	.	miRNA	13836326	13836347	.	-	.	ID=MIMAT0004497;Alias=MIMAT0004497;Name=hsa-miR-24-2-5p;Derives_from=MI0000081
+chr19	.	miRNA_primary_transcript	13836440	13836517	.	-	.	ID=MI0000085;Alias=MI0000085;Name=hsa-mir-27a
+chr19	.	miRNA	13836487	13836508	.	-	.	ID=MIMAT0004501;Alias=MIMAT0004501;Name=hsa-miR-27a-5p;Derives_from=MI0000085
+chr19	.	miRNA	13836447	13836467	.	-	.	ID=MIMAT0000084;Alias=MIMAT0000084;Name=hsa-miR-27a-3p;Derives_from=MI0000085
+chr19	.	miRNA_primary_transcript	13836587	13836659	.	-	.	ID=MI0000079;Alias=MI0000079;Name=hsa-mir-23a
+chr19	.	miRNA	13836630	13836651	.	-	.	ID=MIMAT0004496;Alias=MIMAT0004496;Name=hsa-miR-23a-5p;Derives_from=MI0000079
+chr19	.	miRNA	13836595	13836615	.	-	.	ID=MIMAT0000078;Alias=MIMAT0000078;Name=hsa-miR-23a-3p;Derives_from=MI0000079
+chr19	.	miRNA_primary_transcript	13874699	13874808	.	+	.	ID=MI0000271;Alias=MI0000271;Name=hsa-mir-181c
+chr19	.	miRNA	13874725	13874746	.	+	.	ID=MIMAT0000258;Alias=MIMAT0000258;Name=hsa-miR-181c-5p;Derives_from=MI0000271
+chr19	.	miRNA	13874763	13874784	.	+	.	ID=MIMAT0004559;Alias=MIMAT0004559;Name=hsa-miR-181c-3p;Derives_from=MI0000271
+chr19	.	miRNA_primary_transcript	13874875	13875011	.	+	.	ID=MI0003139;Alias=MI0003139;Name=hsa-mir-181d
+chr19	.	miRNA	13874910	13874932	.	+	.	ID=MIMAT0002821;Alias=MIMAT0002821;Name=hsa-miR-181d-5p;Derives_from=MI0003139
+chr19	.	miRNA	13874953	13874973	.	+	.	ID=MIMAT0026608;Alias=MIMAT0026608;Name=hsa-miR-181d-3p;Derives_from=MI0003139
+chr19	.	miRNA_primary_transcript	14073361	14073479	.	+	.	ID=MI0020340;Alias=MI0020340;Name=hsa-mir-1199
+chr19	.	miRNA	14073381	14073400	.	+	.	ID=MIMAT0031119;Alias=MIMAT0031119;Name=hsa-miR-1199-5p;Derives_from=MI0020340
+chr19	.	miRNA	14073425	14073445	.	+	.	ID=MIMAT0031120;Alias=MIMAT0031120;Name=hsa-miR-1199-3p;Derives_from=MI0020340
+chr19	.	miRNA_primary_transcript	14529543	14529640	.	+	.	ID=MI0003654;Alias=MI0003654;Name=hsa-mir-639
+chr19	.	miRNA	14529603	14529625	.	+	.	ID=MIMAT0003309;Alias=MIMAT0003309;Name=hsa-miR-639;Derives_from=MI0003654
+chr19	.	miRNA_primary_transcript	15179283	15179350	.	-	.	ID=MI0022640;Alias=MI0022640;Name=hsa-mir-6795
+chr19	.	miRNA	15179322	15179345	.	-	.	ID=MIMAT0027490;Alias=MIMAT0027490;Name=hsa-miR-6795-5p;Derives_from=MI0022640
+chr19	.	miRNA	15179283	15179303	.	-	.	ID=MIMAT0027491;Alias=MIMAT0027491;Name=hsa-miR-6795-3p;Derives_from=MI0022640
+chr19	.	miRNA_primary_transcript	15449548	15449608	.	+	.	ID=MI0007075;Alias=MI0007075;Name=hsa-mir-1470
+chr19	.	miRNA	15449548	15449568	.	+	.	ID=MIMAT0007348;Alias=MIMAT0007348;Name=hsa-miR-1470;Derives_from=MI0007075
+chr19	.	miRNA_primary_transcript	18282077	18282161	.	+	.	ID=MI0014232;Alias=MI0014232;Name=hsa-mir-3188
+chr19	.	miRNA	18282129	18282151	.	+	.	ID=MIMAT0015070;Alias=MIMAT0015070;Name=hsa-miR-3188;Derives_from=MI0014232
+chr19	.	miRNA_primary_transcript	18386562	18386634	.	+	.	ID=MI0014233;Alias=MI0014233;Name=hsa-mir-3189
+chr19	.	miRNA	18386607	18386627	.	+	.	ID=MIMAT0015071;Alias=MIMAT0015071;Name=hsa-miR-3189-3p;Derives_from=MI0014233
+chr19	.	miRNA	18386570	18386594	.	+	.	ID=MIMAT0019217;Alias=MIMAT0019217;Name=hsa-miR-3189-5p;Derives_from=MI0014233
+chr19	.	miRNA_primary_transcript	19435063	19435158	.	+	.	ID=MI0003655;Alias=MI0003655;Name=hsa-mir-640
+chr19	.	miRNA	19435123	19435143	.	+	.	ID=MIMAT0003310;Alias=MIMAT0003310;Name=hsa-miR-640;Derives_from=MI0003655
+chr19	.	miRNA_primary_transcript	20399272	20399354	.	-	.	ID=MI0006407;Alias=MI0006407;Name=hsa-mir-1270
+chr19	.	miRNA	20399320	20399342	.	-	.	ID=MIMAT0005924;Alias=MIMAT0005924;Name=hsa-miR-1270;Derives_from=MI0006407
+chr19	.	miRNA_primary_transcript	35122700	35122764	.	+	.	ID=MI0022734;Alias=MI0022734;Name=hsa-mir-6887
+chr19	.	miRNA	35122705	35122727	.	+	.	ID=MIMAT0027674;Alias=MIMAT0027674;Name=hsa-miR-6887-5p;Derives_from=MI0022734
+chr19	.	miRNA	35122744	35122764	.	+	.	ID=MIMAT0027675;Alias=MIMAT0027675;Name=hsa-miR-6887-3p;Derives_from=MI0022734
+chr19	.	miRNA_primary_transcript	35345513	35345627	.	+	.	ID=MI0018175;Alias=MI0018175;Name=hsa-mir-5196
+chr19	.	miRNA	35345541	35345562	.	+	.	ID=MIMAT0021128;Alias=MIMAT0021128;Name=hsa-miR-5196-5p;Derives_from=MI0018175
+chr19	.	miRNA	35345581	35345601	.	+	.	ID=MIMAT0021129;Alias=MIMAT0021129;Name=hsa-miR-5196-3p;Derives_from=MI0018175
+chr19	.	miRNA_primary_transcript	39409623	39409678	.	-	.	ID=MI0016897;Alias=MI0016897;Name=hsa-mir-4530
+chr19	.	miRNA	39409629	39409646	.	-	.	ID=MIMAT0019069;Alias=MIMAT0019069;Name=hsa-miR-4530;Derives_from=MI0016897
+chr19	.	miRNA_primary_transcript	39829716	39829802	.	-	.	ID=MI0022554;Alias=MI0022554;Name=hsa-mir-6719
+chr19	.	miRNA	39829726	39829747	.	-	.	ID=MIMAT0025850;Alias=MIMAT0025850;Name=hsa-miR-6719-3p;Derives_from=MI0022554
+chr19	.	miRNA_primary_transcript	40282543	40282641	.	-	.	ID=MI0003656;Alias=MI0003656;Name=hsa-mir-641
+chr19	.	miRNA	40282603	40282626	.	-	.	ID=MIMAT0003311;Alias=MIMAT0003311;Name=hsa-miR-641;Derives_from=MI0003656
+chr19	.	miRNA_primary_transcript	40369846	40369907	.	+	.	ID=MI0022641;Alias=MI0022641;Name=hsa-mir-6796
+chr19	.	miRNA	40369851	40369873	.	+	.	ID=MIMAT0027492;Alias=MIMAT0027492;Name=hsa-miR-6796-5p;Derives_from=MI0022641
+chr19	.	miRNA	40369887	40369907	.	+	.	ID=MIMAT0027493;Alias=MIMAT0027493;Name=hsa-miR-6796-3p;Derives_from=MI0022641
+chr19	.	miRNA_primary_transcript	41869627	41869698	.	+	.	ID=MI0022642;Alias=MI0022642;Name=hsa-mir-6797
+chr19	.	miRNA	41869632	41869656	.	+	.	ID=MIMAT0027494;Alias=MIMAT0027494;Name=hsa-miR-6797-5p;Derives_from=MI0022642
+chr19	.	miRNA	41869675	41869696	.	+	.	ID=MIMAT0027495;Alias=MIMAT0027495;Name=hsa-miR-6797-3p;Derives_from=MI0022642
+chr19	.	miRNA_primary_transcript	42133445	42133513	.	-	.	ID=MI0015853;Alias=MI0015853;Name=hsa-mir-4323
+chr19	.	miRNA	42133455	42133472	.	-	.	ID=MIMAT0016875;Alias=MIMAT0016875;Name=hsa-miR-4323;Derives_from=MI0015853
+chr19	.	miRNA_primary_transcript	42351131	42351205	.	+	.	ID=MI0025913;Alias=MI0025913;Name=hsa-mir-8077
+chr19	.	miRNA	42351174	42351195	.	+	.	ID=MIMAT0031004;Alias=MIMAT0031004;Name=hsa-miR-8077;Derives_from=MI0025913
+chr19	.	miRNA_primary_transcript	44653686	44653732	.	-	.	ID=MI0016898;Alias=MI0016898;Name=hsa-mir-4531
+chr19	.	miRNA	44653689	44653705	.	-	.	ID=MIMAT0019070;Alias=MIMAT0019070;Name=hsa-miR-4531;Derives_from=MI0016898
+chr19	.	miRNA_primary_transcript	44758657	44758721	.	+	.	ID=MI0025921;Alias=MI0025921;Name=hsa-mir-8085
+chr19	.	miRNA	44758667	44758687	.	+	.	ID=MIMAT0031012;Alias=MIMAT0031012;Name=hsa-miR-8085;Derives_from=MI0025921
+chr19	.	miRNA_primary_transcript	45436654	45436704	.	+	.	ID=MI0020365;Alias=MI0020365;Name=hsa-mir-6088
+chr19	.	miRNA	45436654	45436673	.	+	.	ID=MIMAT0023713;Alias=MIMAT0023713;Name=hsa-miR-6088;Derives_from=MI0020365
+chr19	.	miRNA_primary_transcript	45638994	45639087	.	-	.	ID=MI0000803;Alias=MI0000803;Name=hsa-mir-330
+chr19	.	miRNA	45639049	45639070	.	-	.	ID=MIMAT0004693;Alias=MIMAT0004693;Name=hsa-miR-330-5p;Derives_from=MI0000803
+chr19	.	miRNA	45639009	45639031	.	-	.	ID=MIMAT0000751;Alias=MIMAT0000751;Name=hsa-miR-330-3p;Derives_from=MI0000803
+chr19	.	miRNA_primary_transcript	45674928	45675024	.	+	.	ID=MI0003657;Alias=MI0003657;Name=hsa-mir-642a
+chr19	.	miRNA	45674943	45674964	.	+	.	ID=MIMAT0003312;Alias=MIMAT0003312;Name=hsa-miR-642a-5p;Derives_from=MI0003657
+chr19	.	miRNA	45674978	45674999	.	+	.	ID=MIMAT0020924;Alias=MIMAT0020924;Name=hsa-miR-642a-3p;Derives_from=MI0003657
+chr19	.	miRNA_primary_transcript	45674932	45675008	.	-	.	ID=MI0016685;Alias=MI0016685;Name=hsa-mir-642b
+chr19	.	miRNA	45674941	45674962	.	-	.	ID=MIMAT0018444;Alias=MIMAT0018444;Name=hsa-miR-642b-3p;Derives_from=MI0016685
+chr19	.	miRNA	45674978	45674999	.	-	.	ID=MIMAT0022736;Alias=MIMAT0022736;Name=hsa-miR-642b-5p;Derives_from=MI0016685
+chr19	.	miRNA_primary_transcript	46018932	46019049	.	+	.	ID=MI0003834;Alias=MI0003834;Name=hsa-mir-769
+chr19	.	miRNA	46018961	46018982	.	+	.	ID=MIMAT0003886;Alias=MIMAT0003886;Name=hsa-miR-769-5p;Derives_from=MI0003834
+chr19	.	miRNA	46019000	46019022	.	+	.	ID=MIMAT0003887;Alias=MIMAT0003887;Name=hsa-miR-769-3p;Derives_from=MI0003834
+chr19	.	miRNA_primary_transcript	46709282	46709354	.	-	.	ID=MI0014234;Alias=MI0014234;Name=hsa-mir-320e
+chr19	.	miRNA	46709294	46709311	.	-	.	ID=MIMAT0015072;Alias=MIMAT0015072;Name=hsa-miR-320e;Derives_from=MI0014234
+chr19	.	miRNA_primary_transcript	47226942	47227021	.	+	.	ID=MI0014235;Alias=MI0014235;Name=hsa-mir-3190
+chr19	.	miRNA	47226955	47226974	.	+	.	ID=MIMAT0015073;Alias=MIMAT0015073;Name=hsa-miR-3190-5p;Derives_from=MI0014235
+chr19	.	miRNA	47226988	47227010	.	+	.	ID=MIMAT0022839;Alias=MIMAT0022839;Name=hsa-miR-3190-3p;Derives_from=MI0014235
+chr19	.	miRNA_primary_transcript	47226944	47227019	.	-	.	ID=MI0014236;Alias=MI0014236;Name=hsa-mir-3191
+chr19	.	miRNA	47226952	47226974	.	-	.	ID=MIMAT0015075;Alias=MIMAT0015075;Name=hsa-miR-3191-3p;Derives_from=MI0014236
+chr19	.	miRNA	47226990	47227011	.	-	.	ID=MIMAT0022732;Alias=MIMAT0022732;Name=hsa-miR-3191-5p;Derives_from=MI0014236
+chr19	.	miRNA_primary_transcript	49009906	49009972	.	+	.	ID=MI0022643;Alias=MI0022643;Name=hsa-mir-6798
+chr19	.	miRNA	49009911	49009933	.	+	.	ID=MIMAT0027496;Alias=MIMAT0027496;Name=hsa-miR-6798-5p;Derives_from=MI0022643
+chr19	.	miRNA	49009952	49009972	.	+	.	ID=MIMAT0027497;Alias=MIMAT0027497;Name=hsa-miR-6798-3p;Derives_from=MI0022643
+chr19	.	miRNA_primary_transcript	49308797	49308868	.	-	.	ID=MI0015854;Alias=MI0015854;Name=hsa-mir-4324
+chr19	.	miRNA	49308807	49308826	.	-	.	ID=MIMAT0016876;Alias=MIMAT0016876;Name=hsa-miR-4324;Derives_from=MI0015854
+chr19	.	miRNA_primary_transcript	49500785	49500868	.	-	.	ID=MI0000479;Alias=MI0000479;Name=hsa-mir-150
+chr19	.	miRNA	49500832	49500853	.	-	.	ID=MIMAT0000451;Alias=MIMAT0000451;Name=hsa-miR-150-5p;Derives_from=MI0000479
+chr19	.	miRNA	49500797	49500818	.	-	.	ID=MIMAT0004610;Alias=MIMAT0004610;Name=hsa-miR-150-3p;Derives_from=MI0000479
+chr19	.	miRNA_primary_transcript	49682117	49682195	.	+	.	ID=MI0017977;Alias=MI0017977;Name=hsa-mir-5088
+chr19	.	miRNA	49682122	49682145	.	+	.	ID=MIMAT0021080;Alias=MIMAT0021080;Name=hsa-miR-5088-5p;Derives_from=MI0017977
+chr19	.	miRNA	49682174	49682194	.	+	.	ID=MIMAT0027041;Alias=MIMAT0027041;Name=hsa-miR-5088-3p;Derives_from=MI0017977
+chr19	.	miRNA_primary_transcript	49791866	49791934	.	+	.	ID=MI0022644;Alias=MI0022644;Name=hsa-mir-6799
+chr19	.	miRNA	49791871	49791890	.	+	.	ID=MIMAT0027498;Alias=MIMAT0027498;Name=hsa-miR-6799-5p;Derives_from=MI0022644
+chr19	.	miRNA	49791912	49791934	.	+	.	ID=MIMAT0027499;Alias=MIMAT0027499;Name=hsa-miR-6799-3p;Derives_from=MI0022644
+chr19	.	miRNA_primary_transcript	49832018	49832099	.	+	.	ID=MI0022645;Alias=MI0022645;Name=hsa-mir-6800
+chr19	.	miRNA	49832022	49832042	.	+	.	ID=MIMAT0027500;Alias=MIMAT0027500;Name=hsa-miR-6800-5p;Derives_from=MI0022645
+chr19	.	miRNA	49832076	49832096	.	+	.	ID=MIMAT0027501;Alias=MIMAT0027501;Name=hsa-miR-6800-3p;Derives_from=MI0022645
+chr19	.	miRNA_primary_transcript	49854591	49854651	.	+	.	ID=MI0017388;Alias=MI0017388;Name=hsa-mir-4749
+chr19	.	miRNA	49854593	49854614	.	+	.	ID=MIMAT0019885;Alias=MIMAT0019885;Name=hsa-miR-4749-5p;Derives_from=MI0017388
+chr19	.	miRNA	49854632	49854651	.	+	.	ID=MIMAT0019886;Alias=MIMAT0019886;Name=hsa-miR-4749-3p;Derives_from=MI0017388
+chr19	.	miRNA_primary_transcript	49888175	49888230	.	+	.	ID=MI0017389;Alias=MI0017389;Name=hsa-mir-4750
+chr19	.	miRNA	49888177	49888198	.	+	.	ID=MIMAT0019887;Alias=MIMAT0019887;Name=hsa-miR-4750-5p;Derives_from=MI0017389
+chr19	.	miRNA	49888209	49888230	.	+	.	ID=MIMAT0022979;Alias=MIMAT0022979;Name=hsa-miR-4750-3p;Derives_from=MI0017389
+chr19	.	miRNA_primary_transcript	49933064	49933137	.	+	.	ID=MI0017390;Alias=MI0017390;Name=hsa-mir-4751
+chr19	.	miRNA	49933073	49933096	.	+	.	ID=MIMAT0019888;Alias=MIMAT0019888;Name=hsa-miR-4751;Derives_from=MI0017390
+chr19	.	miRNA_primary_transcript	51206929	51207009	.	-	.	ID=MI0025910;Alias=MI0025910;Name=hsa-mir-8074
+chr19	.	miRNA	51206939	51206962	.	-	.	ID=MIMAT0031001;Alias=MIMAT0031001;Name=hsa-miR-8074;Derives_from=MI0025910
+chr19	.	miRNA_primary_transcript	51692612	51692681	.	+	.	ID=MI0000746;Alias=MI0000746;Name=hsa-mir-99b
+chr19	.	miRNA	51692618	51692639	.	+	.	ID=MIMAT0000689;Alias=MIMAT0000689;Name=hsa-miR-99b-5p;Derives_from=MI0000746
+chr19	.	miRNA	51692656	51692677	.	+	.	ID=MIMAT0004678;Alias=MIMAT0004678;Name=hsa-miR-99b-3p;Derives_from=MI0000746
+chr19	.	miRNA_primary_transcript	51692786	51692864	.	+	.	ID=MI0000066;Alias=MI0000066;Name=hsa-let-7e
+chr19	.	miRNA	51692793	51692814	.	+	.	ID=MIMAT0000066;Alias=MIMAT0000066;Name=hsa-let-7e-5p;Derives_from=MI0000066
+chr19	.	miRNA	51692838	51692859	.	+	.	ID=MIMAT0004485;Alias=MIMAT0004485;Name=hsa-let-7e-3p;Derives_from=MI0000066
+chr19	.	miRNA_primary_transcript	51693254	51693339	.	+	.	ID=MI0000469;Alias=MI0000469;Name=hsa-mir-125a
+chr19	.	miRNA	51693268	51693291	.	+	.	ID=MIMAT0000443;Alias=MIMAT0000443;Name=hsa-miR-125a-5p;Derives_from=MI0000469
+chr19	.	miRNA	51693306	51693327	.	+	.	ID=MIMAT0004602;Alias=MIMAT0004602;Name=hsa-miR-125a-3p;Derives_from=MI0000469
+chr19	.	miRNA_primary_transcript	52222020	52222098	.	+	.	ID=MI0022646;Alias=MI0022646;Name=hsa-mir-6801
+chr19	.	miRNA	52222025	52222047	.	+	.	ID=MIMAT0027502;Alias=MIMAT0027502;Name=hsa-miR-6801-5p;Derives_from=MI0022646
+chr19	.	miRNA	52222074	52222093	.	+	.	ID=MIMAT0027503;Alias=MIMAT0027503;Name=hsa-miR-6801-3p;Derives_from=MI0022646
+chr19	.	miRNA_primary_transcript	52281797	52281893	.	+	.	ID=MI0003658;Alias=MI0003658;Name=hsa-mir-643
+chr19	.	miRNA	52281857	52281878	.	+	.	ID=MIMAT0003313;Alias=MIMAT0003313;Name=hsa-miR-643;Derives_from=MI0003658
+chr19	.	miRNA_primary_transcript	53666679	53666762	.	+	.	ID=MI0003140;Alias=MI0003140;Name=hsa-mir-512-1
+chr19	.	miRNA	53666692	53666714	.	+	.	ID=MIMAT0002822;Alias=MIMAT0002822;Name=hsa-miR-512-5p;Derives_from=MI0003140
+chr19	.	miRNA	53666729	53666750	.	+	.	ID=MIMAT0002823;Alias=MIMAT0002823;Name=hsa-miR-512-3p;Derives_from=MI0003140
+chr19	.	miRNA_primary_transcript	53669157	53669254	.	+	.	ID=MI0003141;Alias=MI0003141;Name=hsa-mir-512-2
+chr19	.	miRNA	53669176	53669198	.	+	.	ID=MIMAT0002822_1;Alias=MIMAT0002822;Name=hsa-miR-512-5p;Derives_from=MI0003141
+chr19	.	miRNA	53669213	53669234	.	+	.	ID=MIMAT0002823_1;Alias=MIMAT0002823;Name=hsa-miR-512-3p;Derives_from=MI0003141
+chr19	.	miRNA_primary_transcript	53671968	53672040	.	+	.	ID=MI0003786;Alias=MI0003786;Name=hsa-mir-1323
+chr19	.	miRNA	53671978	53671999	.	+	.	ID=MIMAT0005795;Alias=MIMAT0005795;Name=hsa-miR-1323;Derives_from=MI0003786
+chr19	.	miRNA_primary_transcript	53674197	53674320	.	+	.	ID=MI0003142;Alias=MI0003142;Name=hsa-mir-498
+chr19	.	miRNA	53674230	53674252	.	+	.	ID=MIMAT0002824;Alias=MIMAT0002824;Name=hsa-miR-498-5p;Derives_from=MI0003142
+chr19	.	miRNA	53674266	53674288	.	+	.	ID=MIMAT0037323;Alias=MIMAT0037323;Name=hsa-miR-498-3p;Derives_from=MI0003142
+chr19	.	miRNA_primary_transcript	53675711	53675797	.	+	.	ID=MI0003143;Alias=MI0003143;Name=hsa-mir-520e
+chr19	.	miRNA	53675764	53675784	.	+	.	ID=MIMAT0002825;Alias=MIMAT0002825;Name=hsa-miR-520e-3p;Derives_from=MI0003143
+chr19	.	miRNA	53675726	53675747	.	+	.	ID=MIMAT0037324;Alias=MIMAT0037324;Name=hsa-miR-520e-5p;Derives_from=MI0003143
+chr19	.	miRNA_primary_transcript	53679003	53679085	.	+	.	ID=MI0003144;Alias=MI0003144;Name=hsa-mir-515-1
+chr19	.	miRNA	53679016	53679039	.	+	.	ID=MIMAT0002826;Alias=MIMAT0002826;Name=hsa-miR-515-5p;Derives_from=MI0003144
+chr19	.	miRNA	53679053	53679074	.	+	.	ID=MIMAT0002827;Alias=MIMAT0002827;Name=hsa-miR-515-3p;Derives_from=MI0003144
+chr19	.	miRNA_primary_transcript	53679940	53680023	.	+	.	ID=MI0003145;Alias=MI0003145;Name=hsa-mir-519e
+chr19	.	miRNA	53679953	53679974	.	+	.	ID=MIMAT0002828;Alias=MIMAT0002828;Name=hsa-miR-519e-5p;Derives_from=MI0003145
+chr19	.	miRNA	53679991	53680012	.	+	.	ID=MIMAT0002829;Alias=MIMAT0002829;Name=hsa-miR-519e-3p;Derives_from=MI0003145
+chr19	.	miRNA_primary_transcript	53682159	53682245	.	+	.	ID=MI0003146;Alias=MI0003146;Name=hsa-mir-520f
+chr19	.	miRNA	53682213	53682234	.	+	.	ID=MIMAT0002830;Alias=MIMAT0002830;Name=hsa-miR-520f-3p;Derives_from=MI0003146
+chr19	.	miRNA	53682173	53682194	.	+	.	ID=MIMAT0026609;Alias=MIMAT0026609;Name=hsa-miR-520f-5p;Derives_from=MI0003146
+chr19	.	miRNA_primary_transcript	53685009	53685091	.	+	.	ID=MI0003147;Alias=MI0003147;Name=hsa-mir-515-2
+chr19	.	miRNA	53685022	53685045	.	+	.	ID=MIMAT0002826_1;Alias=MIMAT0002826;Name=hsa-miR-515-5p;Derives_from=MI0003147
+chr19	.	miRNA	53685059	53685080	.	+	.	ID=MIMAT0002827_1;Alias=MIMAT0002827;Name=hsa-miR-515-3p;Derives_from=MI0003147
+chr19	.	miRNA_primary_transcript	53686469	53686555	.	+	.	ID=MI0003148;Alias=MI0003148;Name=hsa-mir-519c
+chr19	.	miRNA	53686484	53686505	.	+	.	ID=MIMAT0002831;Alias=MIMAT0002831;Name=hsa-miR-519c-5p;Derives_from=MI0003148
+chr19	.	miRNA	53686522	53686543	.	+	.	ID=MIMAT0002832;Alias=MIMAT0002832;Name=hsa-miR-519c-3p;Derives_from=MI0003148
+chr19	.	miRNA_primary_transcript	53688481	53688567	.	+	.	ID=MI0003832;Alias=MI0003832;Name=hsa-mir-1283-1
+chr19	.	miRNA	53688494	53688515	.	+	.	ID=MIMAT0005799;Alias=MIMAT0005799;Name=hsa-miR-1283;Derives_from=MI0003832
+chr19	.	miRNA_primary_transcript	53690881	53690965	.	+	.	ID=MI0003149;Alias=MI0003149;Name=hsa-mir-520a
+chr19	.	miRNA	53690895	53690915	.	+	.	ID=MIMAT0002833;Alias=MIMAT0002833;Name=hsa-miR-520a-5p;Derives_from=MI0003149
+chr19	.	miRNA	53690933	53690954	.	+	.	ID=MIMAT0002834;Alias=MIMAT0002834;Name=hsa-miR-520a-3p;Derives_from=MI0003149
+chr19	.	miRNA_primary_transcript	53694393	53694475	.	+	.	ID=MI0003150;Alias=MI0003150;Name=hsa-mir-526b
+chr19	.	miRNA	53694406	53694428	.	+	.	ID=MIMAT0002835;Alias=MIMAT0002835;Name=hsa-miR-526b-5p;Derives_from=MI0003150
+chr19	.	miRNA	53694443	53694464	.	+	.	ID=MIMAT0002836;Alias=MIMAT0002836;Name=hsa-miR-526b-3p;Derives_from=MI0003150
+chr19	.	miRNA_primary_transcript	53695213	53695293	.	+	.	ID=MI0003151;Alias=MI0003151;Name=hsa-mir-519b
+chr19	.	miRNA	53695225	53695246	.	+	.	ID=MIMAT0005454;Alias=MIMAT0005454;Name=hsa-miR-519b-5p;Derives_from=MI0003151
+chr19	.	miRNA	53695263	53695284	.	+	.	ID=MIMAT0002837;Alias=MIMAT0002837;Name=hsa-miR-519b-3p;Derives_from=MI0003151
+chr19	.	miRNA_primary_transcript	53697533	53697617	.	+	.	ID=MI0003152;Alias=MI0003152;Name=hsa-mir-525
+chr19	.	miRNA	53697547	53697567	.	+	.	ID=MIMAT0002838;Alias=MIMAT0002838;Name=hsa-miR-525-5p;Derives_from=MI0003152
+chr19	.	miRNA	53697584	53697605	.	+	.	ID=MIMAT0002839;Alias=MIMAT0002839;Name=hsa-miR-525-3p;Derives_from=MI0003152
+chr19	.	miRNA_primary_transcript	53698385	53698471	.	+	.	ID=MI0003153;Alias=MI0003153;Name=hsa-mir-523
+chr19	.	miRNA	53698400	53698421	.	+	.	ID=MIMAT0005449;Alias=MIMAT0005449;Name=hsa-miR-523-5p;Derives_from=MI0003153
+chr19	.	miRNA	53698437	53698459	.	+	.	ID=MIMAT0002840;Alias=MIMAT0002840;Name=hsa-miR-523-3p;Derives_from=MI0003153
+chr19	.	miRNA_primary_transcript	53700015	53700101	.	+	.	ID=MI0003154;Alias=MI0003154;Name=hsa-mir-518f
+chr19	.	miRNA	53700030	53700051	.	+	.	ID=MIMAT0002841;Alias=MIMAT0002841;Name=hsa-miR-518f-5p;Derives_from=MI0003154
+chr19	.	miRNA	53700067	53700087	.	+	.	ID=MIMAT0002842;Alias=MIMAT0002842;Name=hsa-miR-518f-3p;Derives_from=MI0003154
+chr19	.	miRNA_primary_transcript	53701227	53701287	.	+	.	ID=MI0003155;Alias=MI0003155;Name=hsa-mir-520b
+chr19	.	miRNA	53701267	53701287	.	+	.	ID=MIMAT0002843;Alias=MIMAT0002843;Name=hsa-miR-520b-3p;Derives_from=MI0003155
+chr19	.	miRNA	53701228	53701248	.	+	.	ID=MIMAT0037325;Alias=MIMAT0037325;Name=hsa-miR-520b-5p;Derives_from=MI0003155
+chr19	.	miRNA_primary_transcript	53702737	53702819	.	+	.	ID=MI0003156;Alias=MI0003156;Name=hsa-mir-518b
+chr19	.	miRNA	53702787	53702808	.	+	.	ID=MIMAT0002844;Alias=MIMAT0002844;Name=hsa-miR-518b;Derives_from=MI0003156
+chr19	.	miRNA_primary_transcript	53706252	53706336	.	+	.	ID=MI0003157;Alias=MI0003157;Name=hsa-mir-526a-1
+chr19	.	miRNA	53706266	53706287	.	+	.	ID=MIMAT0002845;Alias=MIMAT0002845;Name=hsa-miR-526a-5p;Derives_from=MI0003157
+chr19	.	miRNA	53706303	53706324	.	+	.	ID=MIMAT0037326;Alias=MIMAT0037326;Name=hsa-miR-526a-3p;Derives_from=MI0003157
+chr19	.	miRNA_primary_transcript	53707453	53707539	.	+	.	ID=MI0003158;Alias=MI0003158;Name=hsa-mir-520c
+chr19	.	miRNA	53707468	53707489	.	+	.	ID=MIMAT0005455;Alias=MIMAT0005455;Name=hsa-miR-520c-5p;Derives_from=MI0003158
+chr19	.	miRNA	53707506	53707527	.	+	.	ID=MIMAT0002846;Alias=MIMAT0002846;Name=hsa-miR-520c-3p;Derives_from=MI0003158
+chr19	.	miRNA_primary_transcript	53708735	53708835	.	+	.	ID=MI0003159;Alias=MI0003159;Name=hsa-mir-518c
+chr19	.	miRNA	53708758	53708780	.	+	.	ID=MIMAT0002847;Alias=MIMAT0002847;Name=hsa-miR-518c-5p;Derives_from=MI0003159
+chr19	.	miRNA	53708796	53708818	.	+	.	ID=MIMAT0002848;Alias=MIMAT0002848;Name=hsa-miR-518c-3p;Derives_from=MI0003159
+chr19	.	miRNA_primary_transcript	53711002	53711088	.	+	.	ID=MI0003160;Alias=MI0003160;Name=hsa-mir-524
+chr19	.	miRNA	53711017	53711038	.	+	.	ID=MIMAT0002849;Alias=MIMAT0002849;Name=hsa-miR-524-5p;Derives_from=MI0003160
+chr19	.	miRNA	53711054	53711074	.	+	.	ID=MIMAT0002850;Alias=MIMAT0002850;Name=hsa-miR-524-3p;Derives_from=MI0003160
+chr19	.	miRNA_primary_transcript	53712268	53712354	.	+	.	ID=MI0003161;Alias=MI0003161;Name=hsa-mir-517a
+chr19	.	miRNA	53712282	53712303	.	+	.	ID=MIMAT0002851;Alias=MIMAT0002851;Name=hsa-miR-517-5p;Derives_from=MI0003161
+chr19	.	miRNA	53712321	53712342	.	+	.	ID=MIMAT0002852;Alias=MIMAT0002852;Name=hsa-miR-517a-3p;Derives_from=MI0003161
+chr19	.	miRNA_primary_transcript	53713347	53713434	.	+	.	ID=MI0003162;Alias=MI0003162;Name=hsa-mir-519d
+chr19	.	miRNA	53713400	53713421	.	+	.	ID=MIMAT0002853;Alias=MIMAT0002853;Name=hsa-miR-519d-3p;Derives_from=MI0003162
+chr19	.	miRNA	53713361	53713385	.	+	.	ID=MIMAT0026610;Alias=MIMAT0026610;Name=hsa-miR-519d-5p;Derives_from=MI0003162
+chr19	.	miRNA_primary_transcript	53716594	53716680	.	+	.	ID=MI0003163;Alias=MI0003163;Name=hsa-mir-521-2
+chr19	.	miRNA	53716647	53716668	.	+	.	ID=MIMAT0002854;Alias=MIMAT0002854;Name=hsa-miR-521;Derives_from=MI0003163
+chr19	.	miRNA_primary_transcript	53720096	53720182	.	+	.	ID=MI0003164;Alias=MI0003164;Name=hsa-mir-520d
+chr19	.	miRNA	53720111	53720130	.	+	.	ID=MIMAT0002855;Alias=MIMAT0002855;Name=hsa-miR-520d-5p;Derives_from=MI0003164
+chr19	.	miRNA	53720149	53720170	.	+	.	ID=MIMAT0002856;Alias=MIMAT0002856;Name=hsa-miR-520d-3p;Derives_from=MI0003164
+chr19	.	miRNA_primary_transcript	53721076	53721142	.	+	.	ID=MI0003165;Alias=MI0003165;Name=hsa-mir-517b
+chr19	.	miRNA	53721081	53721102	.	+	.	ID=MIMAT0002851_1;Alias=MIMAT0002851;Name=hsa-miR-517-5p;Derives_from=MI0003165
+chr19	.	miRNA	53721118	53721139	.	+	.	ID=MIMAT0002857;Alias=MIMAT0002857;Name=hsa-miR-517b-3p;Derives_from=MI0003165
+chr19	.	miRNA_primary_transcript	53722166	53722255	.	+	.	ID=MI0003166;Alias=MI0003166;Name=hsa-mir-520g
+chr19	.	miRNA	53722220	53722243	.	+	.	ID=MIMAT0002858;Alias=MIMAT0002858;Name=hsa-miR-520g-3p;Derives_from=MI0003166
+chr19	.	miRNA	53722182	53722204	.	+	.	ID=MIMAT0026611;Alias=MIMAT0026611;Name=hsa-miR-520g-5p;Derives_from=MI0003166
+chr19	.	miRNA_primary_transcript	53725442	53725526	.	+	.	ID=MI0003167;Alias=MI0003167;Name=hsa-mir-516b-2
+chr19	.	miRNA	53725457	53725478	.	+	.	ID=MIMAT0002859;Alias=MIMAT0002859;Name=hsa-miR-516b-5p;Derives_from=MI0003167
+chr19	.	miRNA	53725497	53725514	.	+	.	ID=MIMAT0002860;Alias=MIMAT0002860;Name=hsa-miR-516b-3p;Derives_from=MI0003167
+chr19	.	miRNA_primary_transcript	53726922	53726986	.	+	.	ID=MI0003168;Alias=MI0003168;Name=hsa-mir-526a-2
+chr19	.	miRNA	53726928	53726949	.	+	.	ID=MIMAT0002845_1;Alias=MIMAT0002845;Name=hsa-miR-526a-5p;Derives_from=MI0003168
+chr19	.	miRNA_primary_transcript	53729838	53729925	.	+	.	ID=MI0003169;Alias=MI0003169;Name=hsa-mir-518e
+chr19	.	miRNA	53729853	53729874	.	+	.	ID=MIMAT0005450;Alias=MIMAT0005450;Name=hsa-miR-518e-5p;Derives_from=MI0003169
+chr19	.	miRNA	53729891	53729911	.	+	.	ID=MIMAT0002861;Alias=MIMAT0002861;Name=hsa-miR-518e-3p;Derives_from=MI0003169
+chr19	.	miRNA_primary_transcript	53731006	53731090	.	+	.	ID=MI0003170;Alias=MI0003170;Name=hsa-mir-518a-1
+chr19	.	miRNA	53731019	53731038	.	+	.	ID=MIMAT0005457;Alias=MIMAT0005457;Name=hsa-miR-518a-5p;Derives_from=MI0003170
+chr19	.	miRNA	53731056	53731077	.	+	.	ID=MIMAT0002863;Alias=MIMAT0002863;Name=hsa-miR-518a-3p;Derives_from=MI0003170
+chr19	.	miRNA_primary_transcript	53734877	53734963	.	+	.	ID=MI0003171;Alias=MI0003171;Name=hsa-mir-518d
+chr19	.	miRNA	53734892	53734913	.	+	.	ID=MIMAT0005456;Alias=MIMAT0005456;Name=hsa-miR-518d-5p;Derives_from=MI0003171
+chr19	.	miRNA	53734929	53734949	.	+	.	ID=MIMAT0002864;Alias=MIMAT0002864;Name=hsa-miR-518d-3p;Derives_from=MI0003171
+chr19	.	miRNA_primary_transcript	53736845	53736934	.	+	.	ID=MI0003172;Alias=MI0003172;Name=hsa-mir-516b-1
+chr19	.	miRNA	53736860	53736881	.	+	.	ID=MIMAT0002859_1;Alias=MIMAT0002859;Name=hsa-miR-516b-5p;Derives_from=MI0003172
+chr19	.	miRNA	53736905	53736922	.	+	.	ID=MIMAT0002860_1;Alias=MIMAT0002860;Name=hsa-miR-516b-3p;Derives_from=MI0003172
+chr19	.	miRNA_primary_transcript	53739333	53739419	.	+	.	ID=MI0003173;Alias=MI0003173;Name=hsa-mir-518a-2
+chr19	.	miRNA	53739348	53739367	.	+	.	ID=MIMAT0005457_1;Alias=MIMAT0005457;Name=hsa-miR-518a-5p;Derives_from=MI0003173
+chr19	.	miRNA	53739385	53739406	.	+	.	ID=MIMAT0002863_1;Alias=MIMAT0002863;Name=hsa-miR-518a-3p;Derives_from=MI0003173
+chr19	.	miRNA_primary_transcript	53741313	53741407	.	+	.	ID=MI0003174;Alias=MI0003174;Name=hsa-mir-517c
+chr19	.	miRNA	53741332	53741353	.	+	.	ID=MIMAT0002851_2;Alias=MIMAT0002851;Name=hsa-miR-517-5p;Derives_from=MI0003174
+chr19	.	miRNA	53741369	53741390	.	+	.	ID=MIMAT0002866;Alias=MIMAT0002866;Name=hsa-miR-517c-3p;Derives_from=MI0003174
+chr19	.	miRNA_primary_transcript	53742512	53742599	.	+	.	ID=MI0003175;Alias=MI0003175;Name=hsa-mir-520h
+chr19	.	miRNA	53742566	53742587	.	+	.	ID=MIMAT0002867;Alias=MIMAT0002867;Name=hsa-miR-520h;Derives_from=MI0003175
+chr19	.	miRNA_primary_transcript	53748636	53748722	.	+	.	ID=MI0003176;Alias=MI0003176;Name=hsa-mir-521-1
+chr19	.	miRNA	53748689	53748710	.	+	.	ID=MIMAT0002854_1;Alias=MIMAT0002854;Name=hsa-miR-521;Derives_from=MI0003176
+chr19	.	miRNA_primary_transcript	53751211	53751297	.	+	.	ID=MI0003177;Alias=MI0003177;Name=hsa-mir-522
+chr19	.	miRNA	53751226	53751247	.	+	.	ID=MIMAT0005451;Alias=MIMAT0005451;Name=hsa-miR-522-5p;Derives_from=MI0003177
+chr19	.	miRNA	53751264	53751285	.	+	.	ID=MIMAT0002868;Alias=MIMAT0002868;Name=hsa-miR-522-3p;Derives_from=MI0003177
+chr19	.	miRNA_primary_transcript	53752397	53752481	.	+	.	ID=MI0003178;Alias=MI0003178;Name=hsa-mir-519a-1
+chr19	.	miRNA	53752411	53752432	.	+	.	ID=MIMAT0005452;Alias=MIMAT0005452;Name=hsa-miR-519a-5p;Derives_from=MI0003178
+chr19	.	miRNA	53752449	53752470	.	+	.	ID=MIMAT0002869;Alias=MIMAT0002869;Name=hsa-miR-519a-3p;Derives_from=MI0003178
+chr19	.	miRNA_primary_transcript	53754018	53754102	.	+	.	ID=MI0003179;Alias=MI0003179;Name=hsa-mir-527
+chr19	.	miRNA	53754031	53754050	.	+	.	ID=MIMAT0002862;Alias=MIMAT0002862;Name=hsa-miR-527;Derives_from=MI0003179
+chr19	.	miRNA_primary_transcript	53756741	53756830	.	+	.	ID=MI0003180;Alias=MI0003180;Name=hsa-mir-516a-1
+chr19	.	miRNA	53756756	53756778	.	+	.	ID=MIMAT0004770;Alias=MIMAT0004770;Name=hsa-miR-516a-5p;Derives_from=MI0003180
+chr19	.	miRNA	53756801	53756818	.	+	.	ID=MIMAT0006778;Alias=MIMAT0006778;Name=hsa-miR-516a-3p;Derives_from=MI0003180
+chr19	.	miRNA_primary_transcript	53758232	53758318	.	+	.	ID=MI0006430;Alias=MI0006430;Name=hsa-mir-1283-2
+chr19	.	miRNA	53758245	53758266	.	+	.	ID=MIMAT0005799_1;Alias=MIMAT0005799;Name=hsa-miR-1283;Derives_from=MI0006430
+chr19	.	miRNA_primary_transcript	53761133	53761222	.	+	.	ID=MI0003181;Alias=MI0003181;Name=hsa-mir-516a-2
+chr19	.	miRNA	53761148	53761170	.	+	.	ID=MIMAT0004770_1;Alias=MIMAT0004770;Name=hsa-miR-516a-5p;Derives_from=MI0003181
+chr19	.	miRNA	53761193	53761210	.	+	.	ID=MIMAT0006778_1;Alias=MIMAT0006778;Name=hsa-miR-516a-3p;Derives_from=MI0003181
+chr19	.	miRNA_primary_transcript	53762344	53762430	.	+	.	ID=MI0003182;Alias=MI0003182;Name=hsa-mir-519a-2
+chr19	.	miRNA	53762397	53762418	.	+	.	ID=MIMAT0002869_1;Alias=MIMAT0002869;Name=hsa-miR-519a-3p;Derives_from=MI0003182
+chr19	.	miRNA	53762358	53762378	.	+	.	ID=MIMAT0037327;Alias=MIMAT0037327;Name=hsa-miR-519a-2-5p;Derives_from=MI0003182
+chr19	.	miRNA_primary_transcript	53787675	53787741	.	+	.	ID=MI0000779;Alias=MI0000779;Name=hsa-mir-371a
+chr19	.	miRNA	53787680	53787699	.	+	.	ID=MIMAT0004687;Alias=MIMAT0004687;Name=hsa-miR-371a-5p;Derives_from=MI0000779
+chr19	.	miRNA	53787716	53787738	.	+	.	ID=MIMAT0000723;Alias=MIMAT0000723;Name=hsa-miR-371a-3p;Derives_from=MI0000779
+chr19	.	miRNA_primary_transcript	53787677	53787742	.	-	.	ID=MI0017393;Alias=MI0017393;Name=hsa-mir-371b
+chr19	.	miRNA	53787715	53787736	.	-	.	ID=MIMAT0019892;Alias=MIMAT0019892;Name=hsa-miR-371b-5p;Derives_from=MI0017393
+chr19	.	miRNA	53787678	53787700	.	-	.	ID=MIMAT0019893;Alias=MIMAT0019893;Name=hsa-miR-371b-3p;Derives_from=MI0017393
+chr19	.	miRNA_primary_transcript	53787890	53787956	.	+	.	ID=MI0000780;Alias=MI0000780;Name=hsa-mir-372
+chr19	.	miRNA	53787931	53787953	.	+	.	ID=MIMAT0000724;Alias=MIMAT0000724;Name=hsa-miR-372-3p;Derives_from=MI0000780
+chr19	.	miRNA	53787895	53787917	.	+	.	ID=MIMAT0026484;Alias=MIMAT0026484;Name=hsa-miR-372-5p;Derives_from=MI0000780
+chr19	.	miRNA_primary_transcript	53788705	53788773	.	+	.	ID=MI0000781;Alias=MI0000781;Name=hsa-mir-373
+chr19	.	miRNA	53788710	53788731	.	+	.	ID=MIMAT0000725;Alias=MIMAT0000725;Name=hsa-miR-373-5p;Derives_from=MI0000781
+chr19	.	miRNA	53788748	53788770	.	+	.	ID=MIMAT0000726;Alias=MIMAT0000726;Name=hsa-miR-373-3p;Derives_from=MI0000781
+chr19	.	miRNA_primary_transcript	53982307	53982397	.	+	.	ID=MI0005757;Alias=MI0005757;Name=hsa-mir-935
+chr19	.	miRNA	53982362	53982384	.	+	.	ID=MIMAT0004978;Alias=MIMAT0004978;Name=hsa-miR-935;Derives_from=MI0005757
+chr19	.	miRNA_primary_transcript	54282109	54282180	.	+	.	ID=MI0017391;Alias=MI0017391;Name=hsa-mir-4752
+chr19	.	miRNA	54282118	54282139	.	+	.	ID=MIMAT0019889;Alias=MIMAT0019889;Name=hsa-miR-4752;Derives_from=MI0017391
+chr19	.	miRNA_primary_transcript	54645309	54645383	.	+	.	ID=MI0025897;Alias=MI0025897;Name=hsa-mir-8061
+chr19	.	miRNA	54645319	54645339	.	+	.	ID=MIMAT0030988;Alias=MIMAT0030988;Name=hsa-miR-8061;Derives_from=MI0025897
+chr19	.	miRNA_primary_transcript	55123225	55123292	.	-	.	ID=MI0025751;Alias=MI0025751;Name=hsa-mir-7975
+chr19	.	miRNA	55123225	55123242	.	-	.	ID=MIMAT0031178;Alias=MIMAT0031178;Name=hsa-miR-7975;Derives_from=MI0025751
+chr19	.	miRNA_primary_transcript	55230885	55230952	.	-	.	ID=MI0022649;Alias=MI0022649;Name=hsa-mir-6804
+chr19	.	miRNA	55230927	55230947	.	-	.	ID=MIMAT0027508;Alias=MIMAT0027508;Name=hsa-miR-6804-5p;Derives_from=MI0022649
+chr19	.	miRNA	55230885	55230906	.	-	.	ID=MIMAT0027509;Alias=MIMAT0027509;Name=hsa-miR-6804-3p;Derives_from=MI0022649
+chr19	.	miRNA_primary_transcript	55239912	55239976	.	-	.	ID=MI0022647;Alias=MI0022647;Name=hsa-mir-6802
+chr19	.	miRNA	55239952	55239971	.	-	.	ID=MIMAT0027504;Alias=MIMAT0027504;Name=hsa-miR-6802-5p;Derives_from=MI0022647
+chr19	.	miRNA	55239912	55239933	.	-	.	ID=MIMAT0027505;Alias=MIMAT0027505;Name=hsa-miR-6802-3p;Derives_from=MI0022647
+chr19	.	miRNA_primary_transcript	55245186	55245250	.	-	.	ID=MI0022648;Alias=MI0022648;Name=hsa-mir-6803
+chr19	.	miRNA	55245224	55245245	.	-	.	ID=MIMAT0027506;Alias=MIMAT0027506;Name=hsa-miR-6803-5p;Derives_from=MI0022648
+chr19	.	miRNA	55245186	55245207	.	-	.	ID=MIMAT0027507;Alias=MIMAT0027507;Name=hsa-miR-6803-3p;Derives_from=MI0022648
+chr19	.	miRNA_primary_transcript	55388181	55388242	.	+	.	ID=MI0022650;Alias=MI0022650;Name=hsa-mir-6805
+chr19	.	miRNA	55388186	55388207	.	+	.	ID=MIMAT0027510;Alias=MIMAT0027510;Name=hsa-miR-6805-5p;Derives_from=MI0022650
+chr19	.	miRNA	55388220	55388242	.	+	.	ID=MIMAT0027511;Alias=MIMAT0027511;Name=hsa-miR-6805-3p;Derives_from=MI0022650
+chr19	.	miRNA_primary_transcript	58334688	58334751	.	+	.	ID=MI0022651;Alias=MI0022651;Name=hsa-mir-6806
+chr19	.	miRNA	58334693	58334716	.	+	.	ID=MIMAT0027512;Alias=MIMAT0027512;Name=hsa-miR-6806-5p;Derives_from=MI0022651
+chr19	.	miRNA	58334730	58334751	.	+	.	ID=MIMAT0027513;Alias=MIMAT0027513;Name=hsa-miR-6806-3p;Derives_from=MI0022651
+chr19	.	miRNA_primary_transcript	58386770	58386858	.	-	.	ID=MI0017394;Alias=MI0017394;Name=hsa-mir-4754
+chr19	.	miRNA	58386827	58386849	.	-	.	ID=MIMAT0019894;Alias=MIMAT0019894;Name=hsa-miR-4754;Derives_from=MI0017394
+chr19	.	miRNA_primary_transcript	58393364	58393446	.	+	.	ID=MI0033418;Alias=MI0033418;Name=hsa-mir-10394
+chr19	.	miRNA	58393364	58393387	.	+	.	ID=MIMAT0041619;Alias=MIMAT0041619;Name=hsa-miR-10394-5p;Derives_from=MI0033418
+chr19	.	miRNA	58393424	58393446	.	+	.	ID=MIMAT0041620;Alias=MIMAT0041620;Name=hsa-miR-10394-3p;Derives_from=MI0033418
+chr19	.	miRNA_primary_transcript	58550285	58550376	.	+	.	ID=MI0022652;Alias=MI0022652;Name=hsa-mir-6807
+chr19	.	miRNA	58550285	58550306	.	+	.	ID=MIMAT0027514;Alias=MIMAT0027514;Name=hsa-miR-6807-5p;Derives_from=MI0022652
+chr19	.	miRNA	58550354	58550376	.	+	.	ID=MIMAT0027515;Alias=MIMAT0027515;Name=hsa-miR-6807-3p;Derives_from=MI0022652
diff --git a/workflow/config.yaml b/workflow/config.yaml
deleted file mode 100644
index 25e52d7e71ae759c66091653bafbc978177d22a3..0000000000000000000000000000000000000000
--- a/workflow/config.yaml
+++ /dev/null
@@ -1,106 +0,0 @@
----
-#### GLOBAL PARAMETERS #####
-
-# Directories
-# Usually there is no need to change these
-map_input_dir: "path/to/map_input_directory" # For the mapping worflow
-quantify_input_dir: "path/to/quantify_input_directory" # For the quantify worflow
-output_dir: "results"
-scripts_dir: "../scripts"
-local_log: "logs/local"
-cluster_log: "logs/cluster"
-
-# Inputs information
-sample: ["sample_1", "sample_2"]  # put all sample names, separated by comma
-
-#######################################################################################################
-####
-#### PREPARE PARAMETERS
-####
-#######################################################################################################
-
-# Isomirs annotation file
-# Number of base pairs to add/substract from 5' (start) and 3' (end) coordinates.
-bp_5p: [0] # array of numbers, e.g., [-2,-1,0,+1], to include 2 upstream and 1 downstream nts
-bp_3p: [0] # array of numbers, e.g., [-2,-1,0,+1], to include 2 upstream and 1 downstream nts
-
-# List of inputs
-organism: ["org/pre"] # e.g., ["homo_sapiens/GRCh38.100", "mus_musculus/GRCm37.98"]
-# this string specifies a path, and the "/" is important for this
-# "pre" specifies the assembly version
-
-
-#### PARAMETERS SPECIFIC TO INPUTS #####
-
-org/pre: # One section for each list item in "organism"; entry should match precisely what
-# is in the "organism" section above, one entry per list item above, omitting the ""
-  # URLs to genome, gene & miRNA annotations
-  genome_url: # FTP/HTTP URL to gzipped genome in FASTA format, Ensembl style
-  # e.g. "ftp://ftp.ensembl.org/pub/release-106/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz"
-  gtf_url: # FTP/HTTP URL to gzipped gene annotations in GTF format, Ensembl style
-  # e.g. "ftp://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.chr.gtf.gz"
-  mirna_url: # FTP/HTTP URL to unzipped microRNA annotations in GFF format, miRBase style
-  # e.g. "https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3"
-
-  # Chromosome name mappings between UCSC <-> Ensembl
-  # Other organisms available at: https://github.com/dpryan79/ChromosomeMappings
-  map_chr_url: # FTP/HTTP URL to mapping table
-  # e.g. "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt"
-  # Chromosome name mapping parameters:
-  column: 1 # Column number from input file where to change chromosome name
-  delimiter: "TAB" # Delimiter of the input file
-
-#######################################################################################################
-####
-#### MAP PARAMETERS
-####
-#######################################################################################################
-
-# Resources: genome, transcriptome, genes, miRs
-# All of these are produced by the "prepare" workflow
-genome: "path/to/genome.processed.fa"
-gtf: "path/to/gene_annotations.filtered.gtf"
-transcriptome: "path/to/transcriptome_idtrim.fa"
-transcriptome_index_segemehl: "path/to/transcriptome_index_segemehl.idx"
-genome_index_segemehl: "path/to/genome_index_segemehl.idx"
-exons: "path/to/exons.bed"
-header_of_collapsed_fasta: "path/to/headerOfCollapsedFasta.sam"
-
-# Tool parameters: quality filter
-q_value: 10  # Q (Phred) score; minimum quality score to keep
-p_value: 50  # minimum % of bases that must have Q quality
-
-# Tool parameters: adapter removal
-error_rate: 0.1  # fraction of allowed errors
-minimum_length: 15  # discard processed reads shorter than the indicated length
-overlap: 3  # minimum overlap length of adapter and read to trim the bases
-max_n: 0  # discard reads containing more than the indicated number of N bases
-
-# Tool parameters: mapping
-max_length_reads: 30  # maximum length of processed reads to map with oligomap
-nh: 100  # discard reads with more mappings than the indicated number
-
-
-#### PARAMETERS SPECIFIC TO INPUTS ####
-
-sample_1:  # one section per list item in "sample"; names have to match
-    adapter: "XXXXXXXXXXXXXXXXXXXX"  # 3' adapter sequence to trim
-    format: "fa"  # file format; currently supported: "fa"
-
-
-#######################################################################################################
-####
-#### QUANTIFY PARAMETERS
-####
-#######################################################################################################
-
-
-# Types of miRNAs to quantify
-# Remove miRNA types you are not interested in
-mir_list: ["miRNA", "miRNA_primary_transcript", "isomirs"]
-
-# Resources: miR annotations, chromosome name mappings
-# All of these are produced by the "prepare" workflow
-mirnas_anno: "path/to/mirna_filtered.bed"
-isomirs_anno: "path/to/isomirs_annotation.bed"
-...
\ No newline at end of file
diff --git a/workflow/rules/prepare.smk b/workflow/rules/prepare.smk
index 2e4c1913b58171b79d95f75b01ec9c9571107a7b..f16c715df8cad8ef00d7d6253814663215ee9e8c 100644
--- a/workflow/rules/prepare.smk
+++ b/workflow/rules/prepare.smk
@@ -32,9 +32,6 @@ localrules:
     finish_prepare,
     genome_process,
     filter_anno_gtf,
-    mirna_anno,
-    dict_chr,
-
 
 ###############################################################################
 ### Finish rule
@@ -103,14 +100,14 @@ rule genome_process:
             config["output_dir"], "{organism}", "genome.processed.fa"
         ),
     params:
-        url=lambda wildcards: config[wildcards.organism]["genome_url"],
+        path=lambda wildcards: config[wildcards.organism]["genome_path"],
         dir_out=os.path.join(config["output_dir"], "{organism}"),
     log:
         os.path.join(config["local_log"], "{organism}", "genome_process.log"),
     singularity:
         "docker://zavolab/ubuntu:18.04"
     shell:
-        "(bash {input.script} {params.dir_out} {log} {params.url})"
+        "(bash {input.script} {params.dir_out} {log} {params.path})"
 
 
 ###############################################################################
@@ -128,14 +125,14 @@ rule filter_anno_gtf:
             "gene_annotations.filtered.gtf",
         ),
     params:
-        url=lambda wildcards: config[wildcards.organism]["gtf_url"],
+        path=lambda wildcards: config[wildcards.organism]["gtf_path"],
         dir_out=os.path.join(config["output_dir"], "{organism}"),
     log:
         os.path.join(config["local_log"], "{organism}", "filter_anno_gtf.log"),
     singularity:
         "docker://zavolab/ubuntu:18.04"
     shell:
-        "(bash {input.script} {params.dir_out} {log} {params.url}) &> {log}"
+        "(bash {input.script} {params.dir_out} {log} {params.path}) &> {log}"
 
 
 ###############################################################################
@@ -370,73 +367,15 @@ rule create_header_genome:
 
 
 ###############################################################################
-### Download miRNA annotation
-###############################################################################
-
-
-rule mirna_anno:
-    input:
-        genome=os.path.join(
-            config["output_dir"], "{organism}", "genome.processed.fa"
-        ),
-    output:
-        anno=os.path.join(
-            config["output_dir"], "{organism}", "raw", "mirna.gff3"
-        ),
-    params:
-        anno=lambda wildcards: config[wildcards.organism]["mirna_url"],
-        cluster_log=os.path.join(
-            config["cluster_log"], "{organism}", "mirna_anno.log"
-        ),
-    log:
-        os.path.join(config["local_log"], "{organism}", "mirna_anno.log"),
-    singularity:
-        "docker://zavolab/ubuntu:18.04"
-    shell:
-        "(wget {params.anno} -O {output.anno}) &> {log}"
-
-
-###############################################################################
-### Download dictionary mapping chr
-###############################################################################
-
-
-rule dict_chr:
-    input:
-        genome=os.path.join(
-            config["output_dir"], "{organism}", "genome.processed.fa"
-        ),
-    output:
-        map_chr=os.path.join(
-            config["output_dir"], "{organism}", "UCSC2ensembl.txt"
-        ),
-    params:
-        map_chr=lambda wildcards: config[wildcards.organism]["map_chr_url"],
-        cluster_log=os.path.join(
-            config["cluster_log"], "{organism}", "dict_chr.log"
-        ),
-    log:
-        os.path.join(config["local_log"], "{organism}", "dict_chr.log"),
-    singularity:
-        "docker://zavolab/ubuntu:18.04"
-    shell:
-        "(wget {params.map_chr} -O {output.map_chr}) &> {log}"
-
-
-###############################################################################
-### Mapping chromosomes names, UCSC <-> ENSEMBL
+### Mapping chromosomes names, UCSC <-> ENSEMBL, and filtering chromosome
 ###############################################################################
 
 
 rule map_chr_names:
     input:
-        anno=os.path.join(
-            config["output_dir"], "{organism}", "raw", "mirna.gff3"
-        ),
+        anno=lambda wildcards: config[wildcards.organism]["mirna_path"],
+        map_chr=lambda wildcards: config[wildcards.organism]["map_chr_path"],
         script=os.path.join(config["scripts_dir"], "map_chromosomes.pl"),
-        map_chr=os.path.join(
-            config["output_dir"], "{organism}", "UCSC2ensembl.txt"
-        ),
     output:
         gff=os.path.join(
             config["output_dir"], "{organism}", "mirna_chr_mapped.gff3"
@@ -460,7 +399,6 @@ rule map_chr_names:
         {output.gff} \
         ) &> {log}"
 
-
 ###############################################################################
 ### Filtering _1 miR IDs
 ###############################################################################
@@ -520,6 +458,35 @@ rule gfftobed:
         ) &> {log}"
 
 
+###############################################################################
+### Extract mature miRNA
+###############################################################################
+
+
+rule filter_mature_mirs:
+    input:
+        bed=os.path.join(
+            config["output_dir"], "{organism}", "mirna_filtered.bed"
+        ),
+    output:
+        bed=os.path.join(
+            config["output_dir"], "{organism}", "mirna_mature_filtered.bed"
+        ),
+    params:
+        cluster_log=os.path.join(
+            config["cluster_log"], "{organism}", "filter_mature_mirs.log"
+        ),
+        precursor="miRNA_primary_transcript",
+    log:
+        os.path.join(
+            config["local_log"], "{organism}", "filter_mature_mirs.log"
+        ),
+    singularity:
+        "docker://zavolab/ubuntu:18.04"
+    shell:
+        "(grep -v {params.precursor} {input.bed} > {output.bed}) &> {log}"
+
+
 ###############################################################################
 ### Index genome fasta file
 ###############################################################################
@@ -574,35 +541,6 @@ rule extract_chr_len:
         "(cut -f1,2 {input.genome} > {output.chrsize}) &> {log}"
 
 
-###############################################################################
-### Extract mature miRNA
-###############################################################################
-
-
-rule filter_mature_mirs:
-    input:
-        bed=os.path.join(
-            config["output_dir"], "{organism}", "mirna_filtered.bed"
-        ),
-    output:
-        bed=os.path.join(
-            config["output_dir"], "{organism}", "mirna_mature_filtered.bed"
-        ),
-    params:
-        cluster_log=os.path.join(
-            config["cluster_log"], "{organism}", "filter_mature_mirs.log"
-        ),
-        precursor="miRNA_primary_transcript",
-    log:
-        os.path.join(
-            config["local_log"], "{organism}", "filter_mature_mirs.log"
-        ),
-    singularity:
-        "docker://zavolab/ubuntu:18.04"
-    shell:
-        "(grep -v {params.precursor} {input.bed} > {output.bed}) &> {log}"
-
-
 ###############################################################################
 ### Create isomirs annotation file from mature miRNA 
 ###############################################################################
@@ -674,6 +612,9 @@ rule iso_anno_rename:
         ),
         bp_5p=lambda wildcards: wildcards.bp_5p,
         bp_3p=lambda wildcards: wildcards.bp_3p,
+        prefix=os.path.join(
+            config["output_dir"], "{organism}", "iso_anno_5p"
+        ),
     log:
         os.path.join(
             config["local_log"],