Calculate expression with RSEM
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
Input reads for quantification (FASTQ files or BAM file for —alignments mode)
*.{fastq.gz,bam}
index{:bash}
RSEM index
rsem/*
counts_gene{:bash}
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
*.genes.results{:bash}
Expression counts on gene level
*.genes.results
counts_transcript{:bash}
*.isoforms.results{:bash}
Expression counts on transcript level
*.isoforms.results
stat{:bash}
*.stat{:bash}
RSEM statistics
*.stat
logs{:bash}
*.log{:bash}
RSEM logs
*.log
versions_rsem{:bash}
${task.process}{:bash}
:string
The name of the process
rsem{:bash}
The name of the tool
rsem-calculate-expression --version | sed 's/Current version: RSEM v//'{:bash}
:eval
The expression to obtain the version of the tool
versions_star{:bash}
star{:bash}
STAR --version | sed -e "s/STAR_//g"{:bash}
bam_star{:bash}
*.STAR.genome.bam{:bash}
BAM file generated by STAR (optional)
*.STAR.genome.bam
bam_genome{:bash}
${prefix}.genome.bam{:bash}
Genome BAM file (optional)
*.genome.bam
bam_transcript{:bash}
${prefix}.transcript.bam{:bash}
Transcript BAM file (optional)
*.transcript.bam
versions{:bash}
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
