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

]

bam (file)

BAM/SAM file containing read alignments

*.{bam}

annotation (file)

Genomic features annotation in GTF or SAF

*.{gtf,saf}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

counts (file)

Counts of reads mapping to features

*featureCounts.txt

summary (file)

Summary log file

*.featureCounts.txt.summary

versions (file)

File containing software versions

versions.yml
included in
atacseq callingcards chipseq metatdenovo nascent rnaseq rnasplice
author
Github user ntoda03
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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.

http://bioinf.wehi.edu.au/featureCounts http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf 10.1093/bioinformatics/btt656