I have a few questions regarding the motif finding function of HOMER.
1) I'm trying to run an update on the motifs with updateMotifFiles.pl but it's unclear to me how to actually run the file. I tried running the file and the command line says that I need to specify an action with -a, but I checked the HOMER website for information and it wasn't helpful for this program, basically just saying what it does and not what parameters to include. Here's what it says:
Updating Motif Files The updateMotifFiles.pl script is useful for two purposes - it will re-download JASPAR motif matrices and incorporate them in the motif files homer uses. It also provides you an opportunity to add your own motifs in the motif/ directory. Motifs placed in the correct directories in the motif/ folder will be incorporated into the final files.
So I don't know what sort of actions are available or might be required to update.
2) This is a two part question. a) In addition to generally updating the motif files from JASPAR, I'd like to incorporate new motifs, either from JASPAR that aren't included in the HOMER download or from other sites. Building off question 1, I'm not sure how to do this as the HOMER website doesn't provide info as far as I can tell for how to add the file with updateMotifFiles.pl. Do I just add the motif file to the specific directory? b) Is there a HOMER motif format available on websites such as JASPAR or TRANSFAC that I can download and use as opposed to creating a motif file from scratch? I don't even know how to view the motif files downloaded by HOMER.