Homer motif enrichment analysis

usage: homer_motif_scanning.py [-h] [-j JID] -f PEAK_LIST [-m MOTIF_FILE]
                               [-sub MOTIF_SUBSET] [-g GENOME]

optional arguments:
  -h, --help            show this help message and exit
  -j JID, --jid JID     enter a job ID, which is used to make a new directory.
                        Every output will be moved into this folder. (default:
                        homer_motif_scanning_yli11_2020-07-28)
  -f PEAK_LIST, --peak_list PEAK_LIST
                        peak_list relative or abs path (default: None)
  -m MOTIF_FILE, --motif_file MOTIF_FILE
                        homer motif file (default: /home/yli11/Data/Motif_data
                        base/Human/homer_format_all.motifs)
  -sub MOTIF_SUBSET, --motif_subset MOTIF_SUBSET
                        subset motifs to annotate (default: None)

Genome Info:
  -g GENOME, --genome GENOME
                        genome version: hg19, hg38, mm9, mm10. currently, only
                        hg19 is available (default: hg19)

Summary

Motif enrichment analysis by Homer.

Default is to use all homer motif (very large collection). You can also use a subset by: (1) provide your own motif file (2) or do a string match in all motifs (see usage)

Input

A list of bed files.

[yli11@nodecn126 gain]$ ls
B_cell_gain.bed  Ery_cell_gain.bed  mono_cell_gain.bed  T_cell_gain.bed
[yli11@nodecn126 gain]$ ls *.bed > peak.list

Usage

hpcf_interactive

module load python/2.7.13

homer_motif_scanning.py -f peak.list -sub MA0139.1,MA0652.1,MA0597.1,MA0080.4,MA0035.3,MA0140.2,MA0694.1,GATA:SCL -g hg19

Output

The output is the same to homer motif discovery.

Summary files

Please find nlogP.summary.csv for log P-value table and Target_percent.summary.csv for %Target.

code @ github.