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HOMER

Motif discovery and next-gen sequencing analysis

http://homer.ucsd.edu/homer/

HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. The module currently only parses output from the findPeaks and TagDirectory tools. If you would like support to be added for other HOMER tools please open a new issue on the MultiQC GitHub page.

FindPeaks​

The HOMER findPeaks MultiQC module parses the summary statistics found at the top of HOMER peak files. Three key statistics are shown in the General Statistics table, all others are saved to multiqc_data/multiqc_homer_findpeaks.txt.

TagDirectory​

The HOMER tag directory submodule parses output from files tag directory output files, generating a number of diagnostic plots.

File search patterns​

homer/FreqDistribution:
  fn: petag.FreqDistribution_1000.txt
homer/GCcontent:
  fn: tagGCcontent.txt
homer/LengthDistribution:
  fn: tagLengthDistribution.txt
homer/RestrictionDistribution:
  fn: petagRestrictionDistribution.*.txt
homer/findpeaks:
  contents: "# HOMER Peaks"
  num_lines: 3
homer/genomeGCcontent:
  fn: genomeGCcontent.txt
homer/tagInfo:
  fn: tagInfo.txt