GimmeMotifs is a motif prediction pipeline.
Project description
Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments.
See full GimmeMotifs documentation for detailed installation instructions and usage examples.
Easy installation
The most straightforward way to install GimmeMotifs is via conda using the bioconda channel.
$ conda install gimmemotifs -c bioconda
Quick start
Download a genome
Create a directory to store genome files.
$ mkdir $HOME/genomes/
To download and index a genome:
$ gimme genome $HOME/genomes/ hg38
Alternatively, you can index a genome directory with chromosome FASTA files on your computer.
$ gimme index /usr/share/genomes/hg19 hg19
Predict some motifs:
$ gimme motifs my_peaks.bed -g hg38 -n my_motifs
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