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Old 11-08-2010, 11:17 AM   #1
VeenaV
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Location: Charlottesville

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Default MACS peaks

Hi,

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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Old 11-08-2010, 12:40 PM   #2
dawe
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Quote:
Originally Posted by VeenaV View Post
Hi,

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
How did you check there's no signal in those regions?
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Old 11-10-2010, 08:46 AM   #3
VeenaV
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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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