Basic Introduction

 

Method

MotifAnalysis1We provide a flexible framework to perform operations related to motif analyses. Currently, the following analyses are available:
Motif Matching: Matches a set of transcription factor motifs found on the main repositories (such as Jaspar, Uniprobe and Hocomoco) against a set of genomic regions of interest.
Motif Enrichment: Performs Fisher’s exact test in order to verify if a set of genomic regions are enriched for particular transcription factors.

 

Download & Install

First, you need to install the package MOODS, which cannot be automatically installed in our setup procedure:

pip install --user https://github.com/fabioticconi/MOODS/tarball/pypi-ready

You can then install the RGT suite:

pip install RGT --user

Further installation instructions, including installation without pip, are found here.

Basic Usage

Download here a simple example of input data for RGT Motif Analysis. Execute the following commands in order to perform a motif matching followed by motif enrichment:

cd RGT_MotifAnalysis_Test
rgt-motifanalysis --matching --input-matrix input_matrix.txt --rand-proportion 10
rgt-motifanalysis --enrichment --input-matrix input_matrix.txt match/random_regions.bed

The matching command will read the experimental matrix, which specifies the PATH to the genomic regions and the genes to make an association test on. It also creates a background made of random regions of size 10% the biggest genomic region in input. It might take between 10 and 30 minutes to run.

The enrichment command will calculate the enrichment statistics for the all the input regions over the random background. This step should take about 5 minutes to complete.

Further usage instructions are found here.