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khb 02-07-2011 01:48 AM

Missing strand _peaks.bed
 
Hi
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
Thanks

ffinkernagel 02-07-2011 02:46 AM

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.

khb 02-07-2011 03:58 AM

Of course. Thanks

rossignol 08-14-2011 11:40 AM

Hi,

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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