Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples.
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README.md

GimmeMotifs

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DOI

Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments.

See full GimmeMotifs documentation for detailed installation instructions and usage examples.

For documentation on the development version see here.

Easy installation

The most straightforward way to install GimmeMotifs is via conda using the bioconda channel.

If you have not used bioconda before, first set up the necessary channels (in this order!). You only have to do this once.

$ conda config --add channels r
$ conda config --add channels defaults
$ conda config --add channels conda-forge
$ conda config --add channels bioconda

You can now install GimmeMotifs with one command:

# Create an environment called gimme with all dependencies
$ conda create -n gimme python=3 gimmemotifs

# Activate the environment
$ conda activate gimme

Python 3 is the preferred version, however, GimmeMotifs also supports Python 2. Don't forget to activate the environment with source activate gimme whenever you want to use GimmeMotifs.

Quick start

Predict some motifs:

$ gimme motifs my_peaks.bed -g /data/genomes/hg38/hg38.fa -n my_motifs

Download a genome

The example above assumes that you have the hg38 genome in /data/genomes/hg38/hg38.fa. GimmeMotifs can also use genomes installed by genomepy.

You can configure the directory where genomepy stores genomes by editing ~/.config/genomepy/genomepy.yaml

genome_dir: /data/genomes

To download a genome from UCSC:

$ genomepy install hg38 UCSC --annotation

Now you can specify this genome for GimmeMotifs by name.

$ gimme motifs my_peaks.bed -g hg38 -n my_motifs

Help