How to create priors from ATAC-seq data for FIMO

[Lucy]

Hi,

I would like to use the create-priors function to generate epigenetic priors from my ATAC-seq data for FIMO.  However, I am confused as to where the FASTA and wiggle files should come from.  Is the FASTA supposed to be the whole genome FASTA that you mapped to?  How do I go about generating a wiggle file - I currently have BAM mapping files, or featureCounts files containing counts within each peak for the different samples.

Thanks very much for the help.

Best wishes,

Lucy  

[cegrant]

The documentation for the create-priors script can be found here:

http://meme-suite.org/doc/create-priors.html

The documentation for the wiggle file format can be found here:

http://genome.ucsc.edu/goldenPath/help/wiggle.html

The FASTA file should be the sequences you want to search using FIMO. The wiggle file should cover a subset of these sequences. You’ll have to write a script to generate the wiggle file from your ATAC-seq data.

It may be helpful to refer to this paper:

Gabriel Cuellar-Partida, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble, and Timothy L. Bailey,

"Epigenetic priors for identifying active transcription factor binding sites",

Bioinformatics 28(1): 56-62, 2012

http://bioinformatics.oxfordjournals.org/content/28/1/56.full.pdf

It describes converting DNase I assay data to priors. Most of the work will be done for you by compute-priors, but you’ll need to convert your ATAC-seq data into a raw score (say read depth at each sequence position), that can be put into wiggle format and used as input to create-priors.