GimmeMotifs is a motif prediction pipeline.
Project description
# GimmeMotifs
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Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments.
See [full GimmeMotifs documentation](http://gimmemotifs.readthedocs.org/) for detailed installation instructions and usage examples.
For documentation on the development version see [here](http://gimmemotifs.readthedocs.org/en/latest/).
## Easy installation
The most straightforward way to install GimmeMotifs is via [conda](https://docs.continuum.io/anaconda/) using the [bioconda](https://bioconda.github.io/) channel. If you have not used bioconda yet, first set up the necessary channels (in this order):
` $ conda config --add channels r $ conda config --add channels defaults $ conda config --add channels conda-forge $ conda config --add channels bioconda `
Now you can create a new environment for GimmeMotifs:
$ conda create -n gimme python=3 gimmemotifs=0.11.0b0
Before using GimmeMotifs activate the environment:
$ source activate gimme
## 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.
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