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.