How to mask motif in HOMER?

Question

[salamandra]

Why when I do this, to mask motif known.1:

findMotifsGenome.pl $PEAK $GENOME $OUT -p 4 -mask $MOTIF

it says: motif not recognized.

I checked the path is correct, so what could else be happening?

[Kevin Blighe]

Hello again

-mask does not take any arguments. It just instructs HOMER to mask repeats and masked (lower case) sequence.

Just run:

findMotifsGenome.pl $PEAK $GENOME $OUT -p 4 -mask

In your output directory will then be a list of motifs present in your genome.

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Edit: I'm aware that the manual states:

Mask motifs ("-mask <motif file="">")

Mask the motif(s) in the supplied motif file before starting motif finding. Multiple motifs can be in the motif file.

The documentation for Homer is not great and often confusing.

Kevin

[h.mon]

Please, show the contents of your bash variables, or show the actual command as it was executed.

Please, show some lines from the motifs file.

Answer 1

[h.mon]

Maybe salamandra needs -maskMotif instead of -motif:

 -maskMotif <motif file1> [motif file 2]... (motifs to mask before motif finding)

[salamandra]

You are right. It's running! Thanks!