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11-08-2010, 11:17 AM
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#1 |
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Junior Member
Location: Charlottesville Join Date: Jul 2010
Posts: 4
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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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11-08-2010, 12:40 PM
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#2 | |
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Senior Member
Location: 45°30'25.22"N / 9°15'53.00"E Join Date: Apr 2009
Posts: 258
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11-10-2010, 08:46 AM
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#3 |
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Junior Member
Location: Charlottesville Join Date: Jul 2010
Posts: 4
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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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