Description

Calculate expression with RSEM

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

reads:file

Input reads for quantification

*.fastq.gz

index:file

RSEM index

rsem/*

Output

name:type
description
pattern

counts_gene

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.genes.results:file

Expression counts on gene level

*.genes.results

counts_transcript

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.isoforms.results:file

Expression counts on transcript level

*.isoforms.results

stat

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.stat:file

RSEM statistics

*.stat

logs

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.log:file

RSEM logs

*.log

versions

versions.yml:file

File containing software versions

versions.yml

bam_star

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.STAR.genome.bam:file

BAM file generated by STAR (optional)

*.STAR.genome.bam

bam_genome

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}.genome.bam:file

Genome BAM file (optional)

*.genome.bam

bam_transcript

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}.transcript.bam:file

Transcript BAM file (optional)

*.transcript.bam

Tools

rseqc
GPL-3.0-or-later

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome