Question regarding CentriMo

[Sylvia Shiah]

Hi,

I was wondering when running CentriMo on a set of differential binding site (chipseq), is it possible to to remove the most matched region (motif) after the first run and re-run it again?

(I'm using the HOCOMOCO human v10 database.)

Thanks,

sylvia

[CharlesEGrant]

There is no option within MEME-ChIP or Centrimo for doing this. You'd have to write your own script, extracting the matches to the motif, masking them in the sequence file, and then rerunning MEME-ChIP or Centrimo.