FIMO motif scanning

usage: motif_scanning.py [-h] [-j JID] -f BED_FILE -m MOTIF_FILE -o OUTPUT
                         [-p FIMO_CUTOFF] [--fimo_addon FIMO_ADDON]
                         [-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_scanning_yli11_2021-05-06)
  -f BED_FILE, --bed_file BED_FILE
                        bed file (default: None)
  -m MOTIF_FILE, --motif_file MOTIF_FILE
                        bed file (default: None)
  -o OUTPUT, --output OUTPUT
                        output csv (default: None)
  -p FIMO_CUTOFF, --fimo_cutoff FIMO_CUTOFF
  --fimo_addon FIMO_ADDON

Genome Info:
  -g GENOME, --genome GENOME
                        genome version: hg19, mm10, mm9, hg38 (default: hg19)
  --genome_fasta GENOME_FASTA
                        genome version: hs, mm (default:
                        /home/yli11/Data/Human/hg19/fasta/hg19.fa)

Summary

FIMO motif scanning

Doc needs to be updated (5/6/2021)

Input

FIMO requires two input files.

The first is genome fasta or any fasta files, you can just use -g hg19, the code will then match the corresponding fasta file.

The second input is the motif file in MEME format.

Usage

hpcf_interactive

module load python/2.7.13

Output

motif mapping bed file

code @ github.