gimmemotifs 0.10.0b6

GimmeMotifs is a motif prediction pipeline.

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.

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.

``$ 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``.

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