Feature/samtools sort after STAR

Sort alignment files with SAMtools instead of STAR. Fixes #182 (closed)

pipeline_documentation.md

@@ -20,6 +20,7 @@ on installation and usage please see [here](README.md).
     - [**create_index_kallisto**](#create_index_kallisto)
     - [**extract_transcripts_as_bed12**](#extract_transcripts_as_bed12)
     - [**fastqc**](#fastqc)
+    - [**sort_genomic_alignment_samtools**](#sort_genomic_alignment_samtools)
     - [**index_genomic_alignment_samtools**](#index_genomic_alignment_samtools)
     - [**star_rpm**](#star_rpm)
     - [**rename_star_rpm_for_alfa**](#rename_star_rpm_for_alfa)
@@ -260,7 +261,7 @@ Sort BAM file with [**SAMtools**](#third-party-software-used).
 - **Input**
   - Alignemnts file (`.bam`); from [**map_genome_star**](#map_genome_star)
 - **Output**
-  - Alignemnts file (`.bam`);
+  - Alignemnts file (`.bam`); used in
 
 #### `index_genomic_alignment_samtools`
 
@@ -291,7 +292,7 @@ Create stranded bedGraph coverage (`.bg`) with
 > assigned to a strand irrespective of its corresponding mate.
 
 - **Input**
-  - Alignments file (`.bam`); from [**map_genome_star**](#map_genome_star)
+  - Alignments file (`.bam`); from [**sort_genomic_alignment_samtools**](#sort_genomic_alignment_samtools)
   - BAM index file (`.bam.bai`); from
     [**index_genomic_alignment_samtools**](#index_genomic_alignment_samtools)
 - **Output**
@@ -356,7 +357,7 @@ Calculates the Transcript Integrity Number (TIN) for each transcript with
 >   is below threshold
 
 - **Input**
-  - Alignments file (`.bam`); from [**map_genome_star**](#map_genome_star)
+  - Alignments file (`.bam`); from [**sort_genomic_alignment_samtools**](#sort_genomic_alignment_samtools)
   - BAM index file (`.bam.bai`); from
     [**index_genomic_alignment_samtools**](#index_genomic_alignment_samtools)
   - Transcript annotations file (12-column `.bed`); from
@@ -628,14 +629,12 @@ Align short reads to reference genome and/or transcriptome with
     - `--outFilterMultimapNmax`: maximum number of multiple alignments allowed; if exceeded, read is considered unmapped; specify in sample table column `multimappers`
 - **Output**
   - Aligned reads file (`.bam`); used in
-    [**calculate_TIN_scores**](#calculate_TIN_scores),
-    [**index_genomic_alignment_samtools**](#index_genomic_alignment_samtools)
-    and [**star_rpm**](#star_rpm)
+    [**sort_genomic_alignment_samtools**](#sort_genomic_alignment_samtools),
   - STAR log file
 - **Non-configurable & non-default**
   - `--outSAMattributes=All`: NH HI AS nM NM MD jM jI MC ch
-  - `--outStd=BAM_SortedByCoordinate`: which output will be directed to `STDOUT` (default 'Log')
-  - `--outSAMtype=BAM SortedByCoordinate`: type of SAM/BAM output (default SAM)
+  - `--outStd=BAM_Unsorted`: which output will be directed to `STDOUT` (default 'Log')
+  - `--outSAMtype=BAM Unsorted`: type of SAM/BAM output (default SAM)
   - `--outSAMattrRGline`: ID:rnaseq_pipeline SM: *sampleID*
 
 #### `quantification_salmon`