---
name: featureCounts
url: http://bioinf.wehi.edu.au/featureCounts/
description: >
  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.
---

The featureCounts module parses results generated by
[featureCounts](http://bioinf.wehi.edu.au/featureCounts/),
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.

As of MultiQC v1.10, the module should also work with output from
[Rsubread](https://bioconductor.org/packages/release/bioc/html/Rsubread.html).
Note that your filenames must end in `.summary` to be discovered.
See [Module search patterns](#module-search-patterns) for how to customise this.

Please note that if files are in "Rsubread mode" then lines will be split by any
whitespace, instead of tab characters. As such, filenames with spaces in will
cause the parsing to fail.
