Fimo output for classes of TFs from specific database

Question

[rbronste]

Currently if getting a fimo database for specific TFs can do the following:

fimo -max-stored-scores 10000000 --thresh 1e-6 -oc /path/to/output/directory -motif /path/to/motif/file \
  /path/to/HOCOMOCOv11_HUMAN_mono_meme_format.meme /path/to/whole_genome.fa

Is there a good way to do this for classes of TFs all at once, for instance if I wanted to look at all Jaspar non redundant vertebrates Forkhead motifs and where they are in mm10 and get an output for the whole subclass instead of one at a time as above?

Thanks!

[ATpoint]

I may point your attention to the FAQs of FIMO. You might read the section on why it is not preferrable to run it on a whole genome fasta, due to the multiple testing problem. Has nothng to do with your question directly, but should be read IMHO.

Answer 1

[Alex Reynolds]

Perhaps take out the --motif argument and pass in a concatenation of the MEME-formatted models. It should treat each model independently. Via: http://meme-suite.org/doc/fimo.html