Thread: _peaks.bed
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Old 02-07-2011, 01:46 AM   #2
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Location: Marburg, Germany

Join Date: Oct 2009
Posts: 110

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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