gimmemotifs 0.10.0b5

GimmeMotifs is a motif prediction pipeline.

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 -c R

Quick start

Download a genome

Create a directory to store genome files.

$ mkdir $HOME/genomes/

To download and index a genome (all UCSC-supported genomes):

$ 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

Frequently Asked Questions (FAQ)

I get the following error: “Invalid value for background argument”.

Currently, this is a bug in the default configuration file. Run gimme motifs with the additional argument -b gc,random.