How to mask motif in HOMER?
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?
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salamandra
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And what is
$MOTIFset to?its the path to the known1.motif file which is saved under 'knownResults' directory after we run findMotifsGenome.pl without the mask motif option. Isn't it the correct file?
You are missing either
-findoption or-optoption (to look for certain motifs) before$MOTIF.That seems to find the genomic positions of the motif. So you're saying that first should find those regions with -find and then run again (to mask the motif) but instead of providing the motif.file as $MOTIF, to provide those regions' file as $MOTIF. Is that it?
it doesn't work either way :( with -find it only gives the regions of the motif
Far as I can tell those two options are exclusive. If you have motifs that you want to optimize then you should use
-optwhich seems to be the case.Maybe I'm not understanding what you mean..but what I want is not to optimize the motif, it's to remove that motif from the analysis. Because, have a situation similar to what's shown in 'Leftover Junk' section in here and want to use the -mask motif.
As there's also another option -mask that simply masks the genome perhaps the command is assuming that is simply -mask without anything in front. In that case, I'm missing some detail.
Not having used homer this part misled me. If you are sure the motifs are in the right format my comments are not relevant.
Do you want to repost original question as a new post and I will delete this one.
What is the content of your motif file? The format syntax is here: http://homer.ucsd.edu/homer/motif/creatingCustomMotifs.html
It can be that the motif(s) that are in your motif file are simply not present in your data.
It seems to have that format It's in my data, the file corresponds to the first motif found by Homer
Then the motif may simply not be present in your input data.
i've re-posted. thanks!
i've reposted. thanks!