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