diff --git a/.gitignore b/.gitignore
index 8b137891791fe96927ad78e64b0aad7bded08bdc..e43b0f988953ae3a84b00331d0ccf5f7d51cb3cf 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1 @@
-
+.DS_Store
diff --git a/prepare_annotation/.gitignore b/prepare_annotation/.gitignore
deleted file mode 100644
index 06cd4097a1ab378199d07c82a5014afbff8d30d0..0000000000000000000000000000000000000000
--- a/prepare_annotation/.gitignore
+++ /dev/null
@@ -1,6 +0,0 @@
-.*
-Log.out
-results
-logs
-dag.png
-nohup.out
diff --git a/prepare_annotation/Snakefile b/prepare_annotation/Snakefile
deleted file mode 100644
index 94c9db71f9be4f40667dd19823ffa3906364c601..0000000000000000000000000000000000000000
--- a/prepare_annotation/Snakefile
+++ /dev/null
@@ -1,177 +0,0 @@
-configfile: "config.yaml"
-
-localrules: download_genome, assemble_genome, download_annotation, assemble_annotation, finish
-
-#################################################################################
-### Final rule
-#################################################################################
-
-rule finish:
- input:
- STAR_index = os.path.join(config["output_dir"], "STAR_index"),
- other_RNA_idx = os.path.join(config["output_dir"], "other_RNAs_sequence.idx"),
- salmon_index = os.path.join(config["output_dir"], "filtered_transcripts_salmon.idx")
-
-#################################################################################
-### Download genome
-#################################################################################
-
-rule download_genome:
- params:
- sequences = expand(config["genome"]),
- output:
- genome_dir = os.path.join(config["output_dir"], "genome")
- singularity:
- "docker://zavolab/ubuntu:18.04"
- log:
- os.path.join(config["local_log"], "download_genome.log")
- shell:
- "(wget --directory-prefix {output.genome_dir} {params.sequences}) &> {log}"
-
-#################################################################################
-### Assemble genome
-#################################################################################
-
-rule assemble_genome:
- input:
- genome_dir = os.path.join(config["output_dir"], "genome")
- output:
- genome = os.path.join(config["output_dir"], "genome.fa")
- params:
- genome = os.path.join(config["output_dir"], "genome.fa.gz")
- singularity:
- "docker://zavolab/ubuntu:18.04"
- log:
- os.path.join(config["local_log"], "assemble_genome.log")
- shell:
- "(cat {input.genome_dir}/* > {params.genome}; \
- zcat {params.genome} | sed \'s/\s.*//\' > {output.genome}; \
- rm {params.genome}; \
- ) &>{log}"
-
-#################################################################################
-### Download annotation
-#################################################################################
-
-rule download_annotation:
- params:
- annotation = expand(config["annotation"]),
- output:
- annotation_dir = os.path.join(config["output_dir"], "annotation")
- singularity:
- "docker://zavolab/ubuntu:18.04"
- log:
- os.path.join(config["local_log"], "download_annotation.log")
- shell:
- "(wget --directory-prefix {output.annotation_dir} {params.annotation}) &> {log}"
-
-#################################################################################
-### Assemble annotation
-#################################################################################
-
-rule assemble_annotation:
- input:
- annotation_dir = os.path.join(config["output_dir"], "annotation")
- output:
- annotation = os.path.join(config["output_dir"], "annotation.gtf")
- params:
- annotation = os.path.join(config["output_dir"], "annotation.gtf.gz")
- singularity:
- "docker://zavolab/ubuntu:18.04"
- log:
- os.path.join(config["local_log"], "assemble_annotation.log")
- shell:
- "(cat {input.annotation_dir}/* > {params.annotation}; \
- zcat {params.annotation} > {output.annotation}; \
- rm {params.annotation}; \
- ) &>{log}"
-
-#################################################################################
-### ToDo: Download other RNA
-#################################################################################
-
-#################################################################################
-### Generate segemehl index for other RNAs
-#################################################################################
-
-rule generate_segemehl_index_other_RNAs:
- input:
- sequence = config["other_RNA"]
- output:
- other_RNA_idx = os.path.join(config["output_dir"], "other_RNAs_sequence.idx")
- log:
- os.path.join(config["local_log"], "generate_segemehl_index_other_RNAs.log")
- singularity:
- "docker://zavolab/segemehl:0.2.0"
- shell:
- "(segemehl.x -x {output.other_RNA_idx} -d {input.sequence}) &> {log}"
-
-#################################################################################
-### Index genome STAR
-#################################################################################
-
-
-
-##################################################################################
-### Filter protein coding and lncRNA transcripts
-##################################################################################
-
-rule filter_transcripts:
- input:
- script = "scripts/fg_extract_transcripts.py",
- annotation = os.path.join(config["output_dir"], "annotation.gtf")
- output:
- annotation = os.path.join(config["output_dir"], "filtered_transcripts.gtf")
- params:
- transcript_biotype = "\"protein_coding,lincRNA,antisense_RNA,retained_intron,sense_intronic\""
- singularity:
- "docker://zavolab/python_htseq:3.6.5_0.10.0"
- log:
- os.path.join(config["local_log"], "filter_transcripts.log")
- shell:
- "(python {input.script} \
- --gtf {input.annotation} \
- --out {output.annotation} \
- --transcript_biotype {params.transcript_biotype}) &> {log}"
-
-##################################################################################
-### Extract transcript sequences
-##################################################################################
-
-rule extract_sequences:
- input:
- annotation = os.path.join(config["output_dir"], "filtered_transcripts.gtf"),
- genome = os.path.join(config["output_dir"], "genome.fa")
- output:
- transcripts = os.path.join(config["output_dir"], "filtered_transcripts.fa")
- singularity:
- "docker://zavolab/cufflinks:2.2.1"
- log:
- os.path.join(config["local_log"],"extract_sequences.log")
- shell:
- "(gffread {input.annotation} \
- -g {input.genome} \
- -w {output.transcripts}) &> {log}"
-
-##################################################################################
-### Index salmon
-##################################################################################
-
-rule index_salmon:
- input:
- transcripts = os.path.join(config["output_dir"], "filtered_transcripts.fa")
- output:
- index = os.path.join(config["output_dir"], "filtered_transcripts_salmon.idx")
- params:
- kmerLen = config["kmerLen"],
- singularity:
- "docker://zavolab/salmon:0.11.0"
- log:
- os.path.join(config["local_log"],"index_salmon.log")
- threads: 8
- shell:
- "(salmon index \
- --transcripts {input.transcripts} \
- --index {output.index} \
- --kmerLen {params.kmerLen} \
- --threads {threads}) &> {log}"
diff --git a/prepare_annotation/cluster.json b/prepare_annotation/cluster.json
deleted file mode 100644
index a6bfdd5fa4aea8da21bdaff8c6f0d0ad96c1c6d8..0000000000000000000000000000000000000000
--- a/prepare_annotation/cluster.json
+++ /dev/null
@@ -1,23 +0,0 @@
-{
- "__default__" :
- {
- "queue": "6hours",
- "time": "05:00:00",
- "threads": "1",
- "mem": "4G",
- "name": "{rule}.{wildcards}",
- "out": "$PWD/logs/cluster_log/{rule}.{wildcards}-%j-%N.out"
- },
- "generate_segemehl_index_other_RNAs":
- {
- "time": "06:00:00",
- "threads":"8",
- "mem":"50G"
- },
- "index_genome_STAR":
- {
- "time": "06:00:00",
- "threads":"8",
- "mem":"75G"
- }
-}
diff --git a/prepare_annotation/config.yaml b/prepare_annotation/config.yaml
deleted file mode 100644
index 92249c924ed5882411b3eb5c031bc74c733b6261..0000000000000000000000000000000000000000
--- a/prepare_annotation/config.yaml
+++ /dev/null
@@ -1,43 +0,0 @@
----
- ##############################################################################
- ### Annotation
- ##############################################################################
- genome: ["ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.3.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.4.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.5.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.6.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.7.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.8.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.9.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.10.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.11.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.12.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.13.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.14.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.15.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.16.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.17.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.18.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.19.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.20.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.21.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.22.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.X.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.Y.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.MT.fa.gz"]
- annotation: ["ftp://ftp.ensembl.org/pub/release-89/gtf/homo_sapiens/Homo_sapiens.GRCh38.89.chr.gtf.gz"]
- other_RNA: "other.fa"
- ##############################################################################
- ### Output and log directories
- ##############################################################################
- output_dir: "results"
- local_log: "logs/local_log"
- cluster_log: "logs/cluster_log"
- ##############################################################################
- ### Options
- ##############################################################################
- sjdbOverhang: 100
- kmerLen: 31
-...
diff --git a/prepare_annotation/other.fa b/prepare_annotation/other.fa
deleted file mode 100644
index 819e24651f2dda9c8f600f98cbd4b62971895822..0000000000000000000000000000000000000000
--- a/prepare_annotation/other.fa
+++ /dev/null
@@ -1,195 +0,0 @@
->RNA45SN1
-GCTGACACGCTGTCCTCTGGCGACCTGTCGCTGGAGAGGTTGGGCCTCCGGATGCGCGCGGGGCTCTGGC
-CTACCGGTGACCCGGCTAGCCGGCCGCGCTCCTGCTTGAGCCGCCTGCCGGGGCCCGCGGGCCTGCTGTT
-CTCTCGCGCGTCCGAGCGTCCCGACTCCCGGTGCCGGCCCGGGTCCGGGTCTCTGACCCACCCGGGGGCG
-GCGGGGAAGGCGGCGAGGGCCACCGTGCCCCCGTGCGCTCTCCGCTGCGGGCGCCCGGGGCGGCCGCGAC
-AACCCCACCCCGCTGGCTCCGTGCCGTGCGTGTCAGGCGTTCTCGTCTCCGCGGGGTTGTCCGCCGCCCC
-TTCCCCGGAGTGGGGGGTTGGCCGGAGCCGATCGGCTCGCTGGCCGGCCGGCCGGCCTCCGCTCCCGGGG
-GGCTCTTCGTGATCGATGTGGTGACGTCGTGCTCTCCCGGGCCGGGTCCGAGCCGCGACGGGCGAGGGGC
-GGACGTTCGTGGCGAACGGGACCGTCCTTCTCGCTCCGCCCCGCGGGGGTCCCCTCGTCTCTCCTCTCCC
-CGCCCGCCGGCGGTGCGTGTGGGAAGGCGTGGGGTGCGGACCCCGGCCCGACCTCGCCGTCCCGCCCGCC
-GCCTTCTGCGTCGCGGGGCGGGCCGGCGGGGTCCTCTGACGCGGCAGACAGCCCTCGCTGTCGCCTCCAG
-TGGTTGTCGACTTGCGGGCGGCCCCCCTCCGCGGCGGTGGGGGTGCCGTCCCGCCGGCCCGTCGTGCTGC
-CCTCTCGGGGGGTTTGCGCGAGCGTCGGCTCCGCCTGGGCCCTTGCGGTGCTCCTGGAGCGCTCCGGGTT
-GTCCCTCAGGTGCCCGAGGCCGAACGGTGGTGTGTCGTTCCCGCCCCCGGCGCCCCCTCCTCCGGTCGCC
-GCCGCGGTGTCCGCGCGTGGGTCCTGAGGGAGCTCGTCGGTGTGGGGTTCGAGGCGGTTTGAGTGAGACG
-AGACGAGACGCGCCCCTCCCACGCGGGGAAGGGCGCCCGCCTGCTCTCGGTGAGCGCACGTCCCGTGCTC
-CCCTCTGGCGGGTGCGCGCGGGCCGTGTGAGCGATCGCGGTGGGTTCGGGCCGGTGTGACGCGTGCGCCG
-GCCGGCCGCCGAGGGGCTGCCGTTCTGCCTCCGACCGGTCGTGTGTGGGTTGACTTCGGAGGCGCTCTGC
-CTCGGAAGGAAGGAGGTGGGTGGACGGGGGGGCCTGGTGGGGTTGCGCGCACGCGCGCACCGGCCGGGCC
-CCCGCCCTGAACGCGAACGCTCGAGGTGGCCGCGCGCAGGTGTTTCCTCGTACCGCAGGGCCCCCTCCCT
-TCCCCAGGCGTCCCTCGGCGCCTCTGCGGGCCCGAGGAGGAGCGGCTGGCGGGTGGGGGGAGTGTGACCC
-ACCCTCGGTGAGAAAAGCCTTCTCTAGCGATCTGAGAGGCGTGCCTTGGGGGTACCGGATCCCCCGGGCC
-GCCGCCTCTGTCTCTGCCTCCGTTATGGTAGCGCTGCCGTAGCGACCCGCTCGCAGAGGACCCTCCTCCG
-CTTCCCCCTCGACGGGGTTGGGGGGGAGAAGCGAGGGTTCCGCCGGCCACCGCGGTGGTGGCCGAGTGCG
-GCTCGTCGCCTACTGTGGCCCGCGCCTCCCCCTTCCGAGTCGGGGGAGGATCCCGCCGGGCCGGGCCCGG
-CGTTCCCAGCGGGTTGGGACGCGGCGGCCGGCGGGCGGTGGGTGTGCGCGCCCGGCGCTCTGTCCGGCGC
-GTGACCCCCTCCGCCGCGAGTCGGCTCTCCGCCCGCTCCCGTGCCGAGTCGTGACCGGTGCCGACGACCG
-CGTTTGCGTGGCACGGGGTCGGGCCCGCCTGGCCCTGGGAAAGCGTCCCACGGTGGGGGCGCGCCGGTCT
-CCCGGAGCGGGACCGGGTCGGAGGATGGACGAGAATCACGAGCGACGGTGGTGCGGGCGTGTCGGGTTCG
-TGGCTGCGGTCGCTCCGGGGCCCCCGGTGGCGGGGCCCCGGGGCTCGCGAGGCGGTTCTCGGTGGGGGCC
-GAGGGCCGTCCGGCGTCCCAGGCGGGGCGCCGCGGGACCGCCCTCGTGTCTGTGGCGGTGGGATCCCGCG
-GCCGTGTTTTCCTGGTGGCCCGGCCGTGCCTGAGGTTTCTCCCCGAGCCGCCGCCTCTGCGGGCTCCCGG
-GTGCCCTTGCCCTCGCGGTCCCCGGCCCTCGCCCGTCTGTGCCCTCTTCCCCGCCCGCCGCCCGCCGATC
-CTCTTCTTCCCCCCGAGCGGCTCACCGGCTTCACGTCCGTTGGTGGCCCCGCCTGGGACCGAACCCGGCA
-CCGCCTCGTGGGGCGCCGCCGCCGGCCACTGATCGGCCCGGCGTCCGCGTCCCCCGGCGCGCGCCTTGGG
-GACCGGGTCGGTGGCGCCCCGCGTGGGGCCCGGTGGGCTTCCCGGAGGGTTCCGGGGGTCGGCCTGCGGC
-GCGTGCGGGGGAGGAGACGGTTCCGGGGGACCGGCCGCGACTGCGGCGGCGGTGGTGGGGGCAGCCGCGG
-GGATCGCCGAGGGCCGGTCGGCCGCCCCGGGTGCCGCGCGGTGCCGCCGGCGGCGGTGAGGCCCCGCGCG
-TGTGTCCCGGCCGCGGTCGGCCGCGCTCGAGGGGTCCCCGTGGCGTCCCCTTCCCCGCCGGCCGCCTTTC
-TCGCGCCTTCCCCGTCGCCCCGGCCTCGCCCGTGGTCTCTCGTCTTCTCCCGGCCCGCTCTTCCGAACCG
-GGTCGGCGCGTCCCCCGGGTGCGCCTCGCTTCCCGGGCCTGCCGCGGCCCTTCCCCGAGGCGTCCGTCCC
-GGGCGTCGGCGTCGGGGAGAGCCCGTCCTCCCCGCGTGGCGTCGCCCCGTTCGGCGCGCGCGTGCGCCCG
-AGCGCGGCCCGGTGGTCCCTGCCGGACAGGCGTTCGTGCGACGTGTGGCGTGGGTCGACCTCCGCCTTGC
-CGGTCGCTCGCCCTTTCCCCGGGTCGGGGGGTGGGGCCCGGGCCGGGGCCTCGGCCCCGGTCGCGGTCCC
-CCGTCCCGGGCGGGGGCGGGCGCGCCGGCCGGCCTCGGTCGGCCCTCCCTTGGCCGTCGTGTGGCGTGTG
-CCACCCCTGCGCCCGCGCCCGCCGGCGGGGCTCGGAGCCGGGCTTCGGCCGGGCCCCGGGCCCTCGACCG
-GACCGGTGCGCGGGCGCTGCGGCCGCACGGCGCGACTGTCCCCGGGCCGGGCACCGCGGTCCGCCTCTCG
-CTCGCCGCCCGGACGTCGGGGCCGCCCCGCGGGGCGGGCGGAGCGCCGTCCCCGCCTCGCCGCCGCCCGC
-GGGCGCCGGCCGCGCGCGCGCGCGCGTGGCCGCCGGTCCCTCCCGGCCGCCGGGCGCGGGTCGGGCCGTC
-CGCCTCCTCGCGGGCGGGCGCGACGAAGAAGCGTCGCGGGTCTGTGGCGCGGGGCCCCGGTGGTCGTGTC
-GCGTGGGGGGCGGGTGGTTGGGGCGTCCGGTTCGCCGCGCCCCGCCCCGGCCCCACCGGTCCCGGCCGCC
-GCCCCCGCGCCCGCTCGCTCCCTCCCGTCCGCCCGTCCGCGGCCCGTCCGTCCGTCCGTCGTCCTCCTCG
-CTTGCGGGGCGCCGGGCCCGTCCTCGCGAGGCCCCCCGGCCGGCCGTCCGGCCGCGTCGGGGCCTCGCCG
-CGCTCTACCTTACCTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATG
-TCTGAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCG
-CTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCC
-TTCGCGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTCAGCCCCTCTCCGGCCCCGGCCGG
-GGGGCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCCCCGTGGCGGCGA
-CGACCCATTCGAACGTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTACCATGGTGACCACGGGT
-GACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCA
-GGCGCGCAAATTACCCACTCCCGACCCGGGGAGGTAGTGACGAAAAATAACAATACAGGACTCTTTCGAG
-GCCCTGTAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCA
-GCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGAT
-CTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGCCACCGCCCGTCCCCGCCCCTTGCCTCTCGGCGCC
-CCCTCGATGCTCTTAGCTGAGTGTCCCGCGGGGCCCGAAGCGTTTACTTTGAAAAAATTAGAGTGTTCAA
-AGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGT
-TTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATT
-CTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAA
-GTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACCGGCGATGCGGC
-GGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGGAGTATGG
-TTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGA
-CTCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCTCGATTC
-CGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAACGA
-GACTCTGGCATGCTAACTAGTTACGCGACCCCCGAGCGGTCGGCGTCCCCCAACTTCTTAGAGGGACAAG
-TGGCGTTCAGCCACCCGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCG
-CGCTACACTGACTGGCTCAGCGTGTGCCTACCCTACGCCGGCAGGCGCGGGTAACCCGTTGAACCCCATT
-CGTGATGGGGATCGGGGATTGCAATTATTCCCCATGAACGAGGAATTCCCAGTAAGTGCGGGTCATAAGC
-TTGCGTTGATTAAGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGGATGGTTTAGTGAG
-GCCCTCGGATCGGCCCCGCCGGGGTCGGCCCACGGCCCTGGCGGAGCGCTGAGAAGACGGTCGAACTTGA
-CTATCTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAACGGAGC
-CCGGAGGGCGAGGCCCGCGGCGGCGCCGCCGCCGCCGCGCGCTTCCCTCCGCACACCCACCCCCCCACCG
-CGACGCGGCGCGTGCGCGGGCGGGGCCCGCGTGCCCGTTCGTTCGCTCGCTCGTTCGTTCGCCGCCCGGC
-CCCGCCGGCCGCGAGAGCCGGAGAACTCGGGAGGGAGACGGGGGAGAGAGAGAGAGAGAGAGAAAGAGAA
-AGAAGGGCGTGTCGTTGGTGTGCGCGTGTCGTGGGGCCGGCGGGCGGCGGGGAGCGGTCCCCGGCCGCGG
-CCCCGACGACGTGGGTGTCGGCGGGCGCGGGGGCGGTTCTCGGCGGCGTCGCGGCGGGTCTGGGGGGGTC
-TCGGTGCCCTCCTCCCCGCCGGGGCCCGTCGTCCGGCCCCGCCGCGCCGGCTCCCCGTCTTCGGGGCCGG
-CCGGATTCCCGTCGCCTCCGCCGCGCCGCTCCGCGCCGCCGGGCACGGCCCCGCTCGCTCTCCCCGGCCT
-TCCCGCTAGGGCGTCTCGAGGGTCGGGGGCCGGACGCCGGTCCCCTCCCCCGCCTCCTCGTCCGCCCCCC
-CGCCGTCCAGGTACCTAGCGCGTTCCGGCGCGGAGGTTTAAAGACCCCTTGGGGGGATCGCCCGTCCGCC
-CGTGGGTCGGGGGCGGTGGTGGGCCCGCGGGGGAGTCCCGTCGGGAGGGGCCCGGCCCCTCCCGCGCCTC
-CACCGCGGACTCCGCTCCCCGGCCGGGGCCGCGCCGCCGCCGCCGCCGCGGCGGCCGTCGGGTGGGGGCT
-TTACCCGGCGGCCGTCGCGCGCCTGCCGCGCGTGTGGCGTGCGCCCCGCGCCGTGGGGGCGGGAACCCCC
-GGGCGCCTGTGGGGTGGTGTCCGCGCTCGCCCCCGCGTGGGCGGCGCGCGCCTCCCCGTGGTGTGAAACC
-TTCCGACCCCTCTCCGGAGTCCGGTCCCGTTTGCTGTCTCGTCTGGCCGGCCTGAGGCAACCCCCTCTCC
-TCTTGGGCGGGGGGGGGGGGGACGTGCCGCGCCAGGAAGGGCCTCCTCCCGGTGCGTCGTCGGGAGCGCC
-CTCGCCAAATCGACCTCGTACGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC
-TAGCTGCGAGAATTAATGTGAATTGCAGGACACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCG
-GGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGCCGATCAATCGCCCCCGGGGGTGCCTCCGGGC
-TCCTCGGGGTGCGCGGCTGGGGGTTCCCTCGCAGGGCCCGCCGGGGGCCCTCCGTCCCCCTAAGCGCAGA
-CCCGGCGGCGTCCGCCCTCCTCTTGCCGCCGCGCCCGCCCCTTCCCCCTCCCCCCGCGGGCCCTGCGTGG
-TCACGCGTCGGGTGGCGGGGGGGAGAGGGGGGCGCGCCCGGCTGAGAGAGACGGGGAGGGCGGCGCCGCC
-GCCGCCCGCGAAGACGGAGAGGGAAAGAGAGAGCCGGCTCGGGCCGAGTTCCCGTGGCCGCCGCCTGCGG
-TCCGGGTTCCTCCCTCGGGGGGCTCCCTCGCGCCGCGCGCGGCTCGGGGTTCGGGGTTCGTCGGCCCCGG
-CCGGGTGGAAGGTCCCGTGCCCGTCGTCGTCGTCGTCGTCGCGCGTCGTCGGCGGTGGGGGCGTGTTGCG
-TGCGGTGTGGTGGTGGGGGAGGAGGAAGGCGGGTCCGGAAGGGGAAGGGTGCCGGCGGGGAGAGAGGGTC
-GGGGGAGCGCGTCCCGGTCGCCGCGGTTCGCCGCCCGCCCCCGGTGGCGGCCCGGCGTCCGGCCGACCGC
-CGCTCCCGCGCCCCTCCTCCTCCCCGCCGCCCCTCCTCCGAGGCCCCGCCCGTCCTCCTCGCCCTCCCCG
-CGCGTACGCGCGCCCGCCCGCCCGGCTCGCCTCGCGGCGCGTCGGCCGGGGCCGGGAGCCCGCCCCGCGG
-CCCGCCCGGCCGCGCCCGTGGCCGCGGCGCCGGGGTTCGCGTGTCCCCGGCGGCGACCCGCGGGACGCCG
-CGGTGTCGTCCGCCGTCGCGCGCCCGCCTCCGGCTCGCGGCCGCGCCGCGCCGCGCCGGGGCCCCGTCCC
-GAGCTTCCGCGTCGGGGCGGGGCGGCTCCGCCGCCGCGTCCTCGGACCCGTCCCCCCGACCTCCGCGGGG
-GAGACGGGTCGGGGCGTGCGGCGCCCGTCCCGCCCCCGGCCCGTGCCCCTCCCTCCGGTCGTCCCGCTCC
-GGCGGGGCGGCGCGGGGGTGCCGCCGGCCGCGCGCTCTCTCTCCCGTCGCCTCTCCCCCTCGCCGGGCCC
-GTCTCCCGACGGAGCGTCGGGCGGGCGGTCGGGCCGGCGCGATTCCGTCCGTCCGTCCGCCGAGCGGCCC
-GTCCCCCTCCGAGACGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCAGCGGA
-GGAGAAGAAACTAACCAGGATTCCCTCAGTAACGGCGAGTGAACAGGGAAGAGCCCAGCGCCGAATCCCC
-GCCCCGCGGCGGGGCGCGGGACATGTGGCGTACGGAAGACCCGCTCCCCGGCGCCGCTCGTGGGGGGCCC
-AAGTCCTTCTGATCGAGGCCCAGCCCGTGGACGGTGTGAGGCCGGTAGCGGCCCCCGGCGCGCCGGGCCC
-GGGTCTTCCCGGAGTCGGGTTGCTTGGGAATGCAGCCCAAAGCGGGTGGTAAACTCCATCTAAGGCTAAA
-TACCGGCACGAGACCGATAGTCAACAAGTACCGTAAGGGAAAGTTGAAAAGAACTTTGAAGAGAGAGTTC
-AAGAGGGCGTGAAACCGTTAAGAGGTAAACGGGTGGGGTCCGCGCAGTCCGCCCGGAGGATTCAACCCGG
-CGGCGGGTCCGGCCGTGTCGGCGGCCCGGCGGATCTTTCCCGCCCCCCGTTCCTCCCGACCCCTCCACCC
-GCCCTCCCTTCCCCCGCCGCCCCTCCTCCTCCTCCCCGGAGGGGGCGGGCTCCGGCGGGTGCGGGGGTGG
-GCGGGCGGGGCCGGGGGTGGGGTCGGCGGGGGACCGTCCCCCGACCGGCGACCGGCCGCCGCCGGGCGCA
-TTTCCACCGCGGCGGTGCGCCGCGACCGGCTCCGGGACGGCTGGGAAGGCCCGGCGGGGAAGGTGGCTCG
-GGGGGCCCCGTCCGTCCGTCCGTCCGTCCTCCTCCTCCCCCGTCTCCGCCCCCCGGCCCCGCGTCCTCCC
-TCGGGAGGGCGCGCGGGTCGGGGCGGCGGCGGCGGCGGCGGTGGCGGCGGCGGCGGCGGCGGCGGGACCG
-AAACCCCCCCCGAGTGTTACAGCCCCCCCGGCAGCAGCACTCGCCGAATCCCGGGGCCGAGGGAGCGAGA
-CCCGTCGCCGCGCTCTCCCCCCTCCCGGCGCCCACCCCCGCGGGGAATCCCCCGCGAGGGGGGTCTCCCC
-CGCGGGGGCGCGCCGGCGTCTCCTCGTGGGGGGGCCGGGCCACCCCTCCCACGGCGCGACCGCTCTCCCA
-CCCCTCCTCCCCGCGCCCCCGCCCCGGCGACGGGGGGGGTGCCGCGCGCGGGTCGGGGGGCGGGGCGGAC
-TGTCCCCAGTGCGCCCCGGGCGGGTCGCGCCGTCGGGCCCGGGGGAGGTTCTCTCGGGGCCACGCGCGCG
-TCCCCCGAAGAGGGGGACGGCGGAGCGAGCGCACGGGGTCGGCGGCGACGTCGGCTACCCACCCGACCCG
-TCTTGAAACACGGACCAAGGAGTCTAACACGTGCGCGAGTCGGGGGCTCGCACGAAAGCCGCCGTGGCGC
-AATGAAGGTGAAGGCCGGCGCGCTCGCCGGCCGAGGTGGGATCCCGAGGCCTCTCCAGTCCGCCGAGGGC
-GCACCACCGGCCCGTCTCGCCCGCCGCGCCGGGGAGGTGGAGCACGAGCGCACGTGTTAGGACCCGAAAG
-ATGGTGAACTATGCCTGGGCAGGGCGAAGCCAGAGGAAACTCTGGTGGAGGTCCGTAGCGGTCCTGACGT
-GCAAATCGGTCGTCCGACCTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTCC
-GAAGTTTCCCTCAGGATAGCTGGCGCTCTCGCAGACCCGACGCACCCCCGCCACGCAGTTTTATCCGGTA
-AAGCGAATGATTAGAGGTCTTGGGGCCGAAACGATCTCAACCTATTCTCAAACTTTAAATGGGTAAGAAG
-CCCGGCTCGCTGGCGTGGAGCCGGGCGTGGAATGCGAGTGCCTAGTGGGCCACTTTTGGTAAGCAGAACT
-GGCGCTGCGGGATGAACCGAACGCCGGGTTAAGGCGCCCGATGCCGACGCTCATCAGACCCCAGAAAAGG
-TGTTGGTTGATATAGACAGCAGGACGGTGGCCATGGAAGTCGGAATCCGCTAAGGAGTGTGTAACAACTC
-ACCTGCCGAATCAACTAGCCCTGAAAATGGATGGCGCTGGAGCGTCGGGCCCATACCCGGCCGTCGCCGG
-CAGTCGAGAGTGGACGGGAGCGGCGGGGGCGGCGCGCGCGCGCGCGCGTGTGGTGTGCGTCGGAGGGCGG
-CGGCGGCGGCGGCGGCGGGGGTGTGGGGTCCTTCCCCCGCCCCCCCCCCCACGCCTCCTCCCCTCCTCCC
-GCCCACGCCCCGCTCCCCGCCCCCGGAGCCCCGCGGACGCTACGCCGCGACGAGTAGGAGGGCCGCTGCG
-GTGAGCCTTGAAGCCTAGGGCGCGGGCCCGGGTGGAGCCGCCGCAGGTGCAGATCTTGGTGGTAGTAGCA
-AATATTCAAACGAGAACTTTGAAGGCCGAAGTGGAGAAGGGTTCCATGTGAACAGCAGTTGAACATGGGT
-CAGTCGGTCCTGAGAGATGGGCGAGCGCCGTTCCGAAGGGACGGGCGATGGCCTCCGTTGCCCTCGGCCG
-ATCGAAAGGGAGTCGGGTTCAGATCCCCGAATCCGGAGTGGCGGAGATGGGCGCCGCGAGGCGTCCAGTG
-CGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGTTCTCTTTTCTTTGTGAAGGGC
-AGGGCGCCCTGGAATGGGTTCGCCCCGAGAGAGGGGCCCGTGCCTTGGAAAGCGTCGCGGTTCCGGCGGC
-GTCCGGTGAGCTCTCGCTGGCCCTTGAAAATCCGGGGGAGAGGGTGTAAATCTCGCGCCGGGCCGTACCC
-ATATCCGCAGCAGGTCTCCAAGGTGAACAGCCTCTGGCATGTTGGAACAATGTAGGTAAGGGAAGTCGGC
-AAGCCGGATCCGTAACTTCGGGATAAGGATTGGCTCTAAGGGCTGGGTCGGTCGGGCTGGGGCGCGAAGC
-GGGGCTGGGCGCGCGCCGCGGCTGGACGAGGCGCCGCCGCCCCCCCCACGCCCGGGGCACCCCCCTCGCG
-GCCCTCCCCCGCCCCACCCCGCGCGCGCCGCTCGCTCCCTCCCCGCCCCGCGCCCTCTCTCTCTCTCTCT
-CCCCCGCTCCCCGTCCTCCCCCCTCCCCGGGGGAGCGCCGCGTGGGGGCGGCGGCGGGGGGAGAAGGGTC
-GGGGCGGCAGGGGCCGGCGGCGGCCCGCCGCGGGGCCCCGGCGGCGGGGGCACGGTCCCCCGCGAGGGGG
-GCCCGGGCACCCGGGGGGCCGGCGGCGGCGGCGACTCTGGACGCGAGCCGGGCCCTTCCCGTGGATCGCC
-CCAGCTGCGGCGGGCGTCGCGGCCGCCCCCGGGGAGCCCGGCGGGCGCCGGCGCGCCCCCCCCCCCACCC
-CACGTCTCGTCGCGCGCGCGTCCGCTGGGGGCGGGGAGCGGTCGGGCGGCGGCGGTCGGCGGGCGGCGGG
-GCGGGGCGGTTCGTCCCCCCGCCCTACCCCCCCGGCCCCGTCCGCCCCCCGTTCCCCCCTCCTCCTCGGC
-GCGCGGCGGCGGCGGCGGGCGGCGGAGGGGCCGCGGGCCGGTCCCCCCCGCCGGGTCCGCCCCCGGGGCC
-GCGGTTCCGCGCGGCGCCTCGCCTCGGCCGGCGCCTAGCAGCCGACTTAGAACTGGTGCGGACCAGGGGA
-ATCCGACTGTTTAATTAAAACAAAGCATCGCGAAGGCCCGCGGCGGGTGTTGACGCGATGTGATTTCTGC
-CCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAATGAAGCGCGGGTAAACGGCGGGAGTAACTATGACTC
-TCTTAAGGTAGCCAAATGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATGAACGAGATTCCCACTG
-TCCCTACCTACTATCCAGCGAAACCACAGCCAAGGGAACGGGCTTGGCGGAATCAGCGGGGAAAGAAGAC
-CCTGTTGAGCTTGACTCTAGTCTGGCACGGTGAAGAGACATGAGAGGTGTAGAATAAGTGGGAGGCCCCC
-GGCGCCCCCCCGGTGTCCCCGCGAGGGGCCCGGGGCGGGGTCCGCCGGCCCTGCGGGCCGCCGGTGAAAT
-ACCACTACTCTGATCGTTTTTTCACTGACCCGGTGAGGCGGGGGGGCGAGCCCCGAGGGGCTCTCGCTTC
-TGGCGCCAAGCGCCCGGCCGCGCGCCGGCCGGGCGCGACCCGCTCCGGGGACAGTGCCAGGTGGGGAGTT
-TGACTGGGGCGGTACACCTGTCAAACGGTAACGCAGGTGTCCTAAGGCGAGCTCAGGGAGGACAGAAACC
-TCCCGTGGAGCAGAAGGGCAAAAGCTCGCTTGATCTTGATTTTCAGTACGAATACAGACCGTGAAAGCGG
-GGCCTCACGATCCTTCTGACCTTTTGGGTTTTAAGCAGGAGGTGTCAGAAAAGTTACCACAGGGATAACT
-GGCTTGTGGCGGCCAAGCGTTCATAGCGACGTCGCTTTTTGATCCTTCGATGTCGGCTCTTCCTATCATT
-GTGAAGCAGAATTCACCAAGCGTTGGATTGTTCACCCACTAATAGGGAACGTGAGCTGGGTTTAGACCGT
-CGTGAGACAGGTTAGTTTTACCCTACTGATGATGTGTTGTTGCCATGGTAATCCTGCTCAGTACGAGAGG
-AACCGCAGGTTCAGACATTTGGTGTATGTGCTTGGCTGAGGAGCCAATGGGGCGAAGCTACCATCTGTGG
-GATTATGACTGAACGCCTCTAAGTCAGAATCCCGCCCAGGCGGAACGATACGGCAGCGCCGCGGAGCCTC
-GGTTGGCCTCGGATAGCCGGTCCCCCGCCTGTCCCCGCCGGCGGGCCGCCCCCCCCTCCACGCGCCCCGC
-GCGCGCGGGAGGGCGCGTGCCCCGCCGCGCGCCGGGACCGGGGTCCGGTGCGGAGTGCCCTTCGTCCTGG
-GAAACGGGGCGCGGCTGGAAAGGCGGCCGCCCCCTCGCCCGTCACGCACCGCACGTTCGTGGGGAACCTG
-GCGCTAAACCATTCGTAGACGACCTGCTTCTGGGTCGGGGTTTCGTACGTAGCAGAGCAGCTCCCTCGCT
-GCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTCCGCGCGCGCGCGCGCGCGTGCGTGCGGGGG
-GCCCGGCGGGGCGTGCGCGTCCGGCGCCGTCCGTCCTTCCGTTCGTCTTCCTCCCTCCCGGCCTCTCCCG
-CCGACCGCGGGCGTGGTGGTGGGGGTGGGGGGGAGGGCGCGCGACCCCGGTCGGCGCGCCCCGCTTCTTC
-GGTTCCCGCCTCCTCCCCGTTCACCGCCGGGGCGGCTCGTCCGCTCCGGGCCGGGACGGGGTCCGGGGAG
-CGTGGTTTGGGAGCCGCGGAGGCGGCCGCGCCGAGCCGGGCCCGTGGCCCGCCGGTCCCCGTCCCGGGGG
-TTGGCCGCGCGGGCCCCGGTGGGGCGGCCACCCGGGGTCCCGGCCCTCGCG
->RNA5S1
-GTCTACGGCCATACCACCCTGAACGCGCCCGATCTCGTCTGATCTCGGAAGCTAAGCAGGGTCGGGCCTG
-GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTT
diff --git a/process_data/.gitignore b/process_data/.gitignore
deleted file mode 100644
index 58c3d7f9d20089761693a491f14ae0626205a9b9..0000000000000000000000000000000000000000
--- a/process_data/.gitignore
+++ /dev/null
@@ -1,7 +0,0 @@
-.*
-Log.out
-results
-logs
-dag.png
-nohup.out
-samples
diff --git a/process_data/create_snakemake_flowchart.sh b/process_data/create_snakemake_flowchart.sh
deleted file mode 100755
index ce71a9a3dcfcd940c55d9568bff4e10bfa670f45..0000000000000000000000000000000000000000
--- a/process_data/create_snakemake_flowchart.sh
+++ /dev/null
@@ -1 +0,0 @@
-snakemake --dag -np | dot -Tpng > dag.png
diff --git a/process_data/run_snakefile.sh b/process_data/run_snakefile.sh
deleted file mode 100755
index ceec8a8493b661eab1c279a7e44a6f82d2d77ba6..0000000000000000000000000000000000000000
--- a/process_data/run_snakefile.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-# set -e
-
-mkdir -p logs/cluster_log
-mkdir -p logs/local_log
-
-snakemake \
---cluster-config cluster.json \
---cluster "sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
---cores 256 \
--p \
---rerun-incomplete \
---use-singularity \
---singularity-args "--bind ${PWD}"
diff --git a/prepare_annotation/scripts/fg_extract_transcripts.py b/scripts/fg_extract_transcripts.py
similarity index 100%
rename from prepare_annotation/scripts/fg_extract_transcripts.py
rename to scripts/fg_extract_transcripts.py
diff --git a/process_data/Snakefile b/snakemake/Snakefile
similarity index 100%
rename from process_data/Snakefile
rename to snakemake/Snakefile
diff --git a/process_data/cluster.json b/snakemake/cluster.json
similarity index 100%
rename from process_data/cluster.json
rename to snakemake/cluster.json
diff --git a/process_data/config.yaml b/snakemake/config.yaml
similarity index 100%
rename from process_data/config.yaml
rename to snakemake/config.yaml
diff --git a/prepare_annotation/create_snakemake_flowchart.sh b/snakemake/create_snakemake_flowchart.sh
similarity index 100%
rename from prepare_annotation/create_snakemake_flowchart.sh
rename to snakemake/create_snakemake_flowchart.sh
diff --git a/process_data/paired_end.snakemake b/snakemake/paired_end.snakemake
similarity index 100%
rename from process_data/paired_end.snakemake
rename to snakemake/paired_end.snakemake
diff --git a/process_data/preprocessing.snakefile b/snakemake/preprocessing.snakefile
similarity index 100%
rename from process_data/preprocessing.snakefile
rename to snakemake/preprocessing.snakefile
diff --git a/prepare_annotation/run_snakefile.sh b/snakemake/run_snakefile.sh
similarity index 100%
rename from prepare_annotation/run_snakefile.sh
rename to snakemake/run_snakefile.sh
diff --git a/process_data/single_end.snakefile b/snakemake/single_end.snakefile
similarity index 100%
rename from process_data/single_end.snakefile
rename to snakemake/single_end.snakefile