hi Dawe, All,
I debugged the issue and found that it was basically an issue with the input file fed to MACS.
I was running MACS on .sam files. The program used to generate signal
files from .sam files excluded repeats (X:A:R tags), whereas MACS
included the repeats in the .sam file. I now reran MACS using the bed
files as input for MACS (instead of .sam files) and it looks fine
now.
Thanks,
Veena
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Originally posted by VeenaV View PostHi,
Am using MACS for the first time. I ran MACS on my sequence data and I find peaks (as listed in the bed file) in regions that have no signal. Why would this be? Has anyone encountered this phenomenon before? Please suggest.
Thanks in advance,
Veena
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