Question: RSAT matrix-scan: how to use oligo frequency files for background reference?
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2.0 years ago by
ktehmsen0
ktehmsen0 wrote:

I'm interested in using rsat matrix-scan (command-line version) to score matches to a positional weight matrix for human regulatory factors. I'd like to use the full genome as a background reference; I found the oligo frequency files for human hg38 at http://rsat.sb-roscoff.fr/htmllink.cgi?title=data&file=data/genomes/Homo_sapiens_GRCh38, but I can't determine how to use these. Why are there 94 files here, and how do I choose one from them as a background file? I thought there would be just one background file ready for use here, and it's not clear to me why there are 94.

*matrix-scan online manual describes background file usage as follows:

Background model specification

The background model can be specified in different ways.

-bgfile

This option allows to enter the background model from a background model file. Background model files are tab-delimited files containing the specification of oligonucleotide frequencies. A Markov model of order m=k-1 is automatically obtained from the frequencies of oligonucleotides of length k. There is thus no need to use the option -markov when the background model is secified with a bg file.

The RSAT data folder contains pre-calibrated background model files for all the supported organisms.*

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