I understand that to run HOMER you need BED files, so could I use the BED output file from "macs2 callpeak" to run "findMotifsGenome.pl"?
Yes, use the -size option to specify the size of the region to consider. As an aside, keep in mind that MACS output consists of two BED files - one is yourSample_summits.bed, the other is yourSample_peaks.narrowPeak. The .narrowPeak file is a 6+4 BED file. You can easily convert it to some other format.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
I finally got HOMER to work and realised that the chromosome column of .bed and narrowPeak files are like "NC_000001.11" but I need them to be chr#. Is there anything I can do to change it?
Also, my narrowPeak file has only 4 columns when it should have 10, does that mean something went wrong during peak call?
This is one reason people learn scripting languages, and this represents a great little exercise that one could use to learn python. There are a variety of ways to solve this problem, but I don't know of one which doesn't involve coding of some kind or another. At the very least you'll need a mapping between the two types of chromosome identifiers. I don't know your skill set, and (gasp) one could even use excel for this (I wouldn't recommend it).
As for why your narrowPeak file has only 4 columns - this is very strange. Which four? I don't know how MACS could find peaks (thus creating a file) and yet leave out the majority of information about them. This sounds like an error. You should investigate further. Do you have a positive control of some kind? Either another data set with known peaks, or some small toy sample data set you can use to verify that you can run the software and get expected results?
Sounds like the issue is with how you ran MACS2. Can you share the command and a glimpse of the files you supplied to MACS2?