homer annotatePeaks.pl: is it possible to adjust the threshold for motif scan?

Question

[changxu.fan]

Dear community,

I'm looking at the manual for annotatePeaks.pl (http://homer.ucsd.edu/homer/ngs/annotation.html), but don't see an option to change the pvalue threshold for motif match. such an option is available for the FIMO tool in the meme suite. I would highly appreciate it if someone with a better eye can spot such a function in the homer suite as well!

Thanks, Fan

Answer 1

[Trivas]

I don't see an option to do it from the command line but it is super easy to filter manually/using R. Is there a reason you want to use Homer over FIMO/memesuite?

[changxu.fan]

Thanks for the comment. I did motif discovery using homer. Couldn't figure out a straightforward way to convert a homer motif to a meme motif. Please let me know if you are aware of software/scripts to do this reliably!!

Best, Fan

[Trivas]

I found this on Github: https://gist.github.com/rtraborn/e395776b965398c54c4d