CisGenome MAT files

[vpimmett]

Hi all!

I am a non-computer person, off the bat. I have been trying to use CisGenome to analyze some ChIP-seq data we've obtained, but I've hit a stumbling block.

What the hell is a MAT file and where do I find them?

I need one for hg18 and dm3 -- are they all the same? Different for every set? Do I make them myself or download them from somewhere? Is there a better program to use for peak calling/annotation and de novo motif search (that can be used by someone who has absolutely no idea how to code)? Help me!

[Richard Finney]

CisGenome uses the "mat" suffix (which is also used by Matlab programs). Cistenome ".mat" files are not Matlab files.

The mat file probably looks like this ...

http://www.biostat.jhsph.edu/~hji/cisgenome/index_files/motif.mat

It is documented here :

http://www.biostat.jhsph.edu/~hji/cisgenome/index_files/manual.htm

Note: motif.mat is the motif matrix. The matrix contains pseudocounts to specify the frequency of A,C,G,T respectively. All cells in the matrix must be bigger than 0. You can use a small number like 0.1 for a rare base and a big number, say 150, for a frequent base. “-c” specifies conservation cutoff. -c 40 means only sites with phastcons score >= 40 are retained. Phastcons score is linearly transformed from [0,1] to [0, 255] in CisGenome.