Calculate expression with RSEM
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/*
counts_gene
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
*.genes.results:file
Expression counts on gene level
*.genes.results
counts_transcript
*.isoforms.results:file
Expression counts on transcript level
*.isoforms.results
stat
*.stat:file
RSEM statistics
*.stat
logs
*.log:file
RSEM logs
*.log
versions
versions.yml:file
File containing software versions
versions.yml
bam_star
*.STAR.genome.bam:file
BAM file generated by STAR (optional)
*.STAR.genome.bam
bam_genome
${prefix}.genome.bam:file
Genome BAM file (optional)
*.genome.bam
bam_transcript
${prefix}.transcript.bam:file
Transcript BAM file (optional)
*.transcript.bam
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
