HOMER
Supported Tool
HOMER is a suite of tools for Motif Discovery and next-gen sequencing analysis.
Description
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. 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 HOMER MultiQC module currently only parses output from the findPeaks tool.
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/findpeaks:
contents: "# HOMER Peaks"
num_lines: 3
homer/GCcontent:
fn: tagGCcontent.txt
homer/genomeGCcontent:
fn: genomeGCcontent.txt
homer/RestrictionDistribution:
fn: petagRestrictionDistribution.*.txt
homer/LengthDistribution:
fn: tagLengthDistribution.txt
homer/tagInfo:
fn: tagInfo.txt
homer/FreqDistribution:
fn: petag.FreqDistribution_1000.txt