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Old 02-07-2011, 01:48 AM   #1
Location: Oslo

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Default Missing strand _peaks.bed

I've tried to analyze my data with MACS, and want the file _peaks.bed that MACS gives. Does anyone know how to know which strand each peak is on? The file only contains
chrom start stop name score

Last edited by khb; 02-07-2011 at 01:59 AM.
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Old 02-07-2011, 02:46 AM   #2
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The answer to your question is 'mu'.

A chipseq peak has no strandedness... in theory, you should only see reads of one strand on one, and of the other strand on the other side, crossing over wherever your protein bound the chromatin (since fragments starting further down on the same strand would not have a protein bound, and would not be visible after the chip). In practice, it's not that clear cut. Nevertheless, the peak does not have a strand.
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Old 02-07-2011, 03:58 AM   #3
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Of course. Thanks
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Old 08-14-2011, 11:40 AM   #4
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I see the point about peaks not having a strand. What should I then submit to HOMER when doing motif analysis? HOMER expects to get a peak file in bed format, with the last column being +/- for the strand of the peak.
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