Call motif footprint from bigwiggle files¶

usage: motif_footprint_from_bw.py [-h] [-j JID] -f INPUT_LIST [-m MOTIF_FILE]
                                  [-c FIMO_CUTOFF] [-g GENOME]
                                  [--genome_fasta GENOME_FASTA]

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:
                        motif_footprint_from_bw_yli11_2020-07-12)
  -f INPUT_LIST, --input_list INPUT_LIST
                        tsv 3 columns, bed,bw,outputname (default: None)
  -m MOTIF_FILE, --motif_file MOTIF_FILE
                        motif file, use absolute path (default: /home/yli11/Da
                        ta/Motif_database/Human/homer_jaspar.meme)
  -c FIMO_CUTOFF, --fimo_cutoff FIMO_CUTOFF

Genome Info:
  -g GENOME, --genome GENOME
                        genome version: hg19, mm10, mm9 (default: hg19)
  --genome_fasta GENOME_FASTA
                        genome version: hs, mm (default:
                        /home/yli11/Data/Human/hg19/fasta/hg19.fa)

Summary¶

This pipeline is designed as the next step after ATAC-seq footprint pipeline. Given motif pwm file, we first perform motif scanning on the given peak file, we then extract Tn5 cutting frequency from the bw file. A valid motif footprint should be a U-shape (i.e., mean frequency inside the motif is smaller than the flanking regions).

Input¶

The input file is a tsv format containing 3 columns: bed file, bw file, output-prefix.

For bed file, either relative path or absolute path is OK.

For bw file, it needs absolute path.

H2.narrowPeak   /path/to/H2.bw  Hudep2_footprints
H1.narrowPeak   /path/to/H1.bw  Hudep1_footprints

Usage¶

module load python/2.7.13

motif_footprint_from_bw.py -f input.list

For mouse genome

module load python/2.7.13

motif_footprint_from_bw.py -f input.list -g mm9 -m /home/yli11/Data/Motif_database/Mouse/mouse_TF.meme

Output¶

Each line will have its own result dir in the jobID folder.

Individual motif footprint result is shown in jobID/output_name/FIMO_motif_mapping/ directory.

In each motif folder, you can find:

the exact mapped location: fimo.cuts.freq.txt.filtered_fimo.bed
the average footprint signal plot: motif_name.footprint.png.

If there’s a motif that you are interested in, there’s a script for you to generate a footprint heatmap plot: signal_plot.sh, which you just need to run bash signal_plot.sh.

“NFIX”,”PU.1”,”CTCF”,”GATA1”,”ZBTB7A” will be automatically generated since they are used very often in our projects.

code @ github.