Description

Count reads that map to genomic features

Input

name:type
description
pattern

meta:map

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

]

bams:file

BAM files containing mapped reads

*.bam

annotation:file

Genomic features annotation in GTF or SAF

*.{gtf,saf}

Output

name:type
description
pattern

counts

meta:map

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

]

*featureCounts.txt:file

Counts of reads mapping to features

*featureCounts.txt

summary

meta:map

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

]

*featureCounts.txt.summary:file

Summary log file

*.featureCounts.txt.summary

versions

versions.yml:file

File containing software versions

versions.yml

Tools

featurecounts
GPL v3

featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads.