Gimmemotifs

Introduction

GimmeMotifs is a suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/gimmemotifs

Home page: https://github.com/vanheeringen-lab/gimmemotifs

Versions

• 0.17.1

Commands

• gimme

Module

You can load the modules by:

module load biocontainers
module load gimmemotifs

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run gimmemotifs on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=gimmemotifs
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers gimmemotifs

gimme motifs ENCFF407IVS.bed ENCFF407IVS_motifs \
    -g ~/.local/share/genomes/hg38/hg38.fa --denovo