_peaks.bed

khb · 02-07-2011, 01:48 AM

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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02-07-2011, 01:48 AM	#1
khb Member Location: Oslo Join Date: Dec 2010 Posts: 15	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 Last edited by khb; 02-07-2011 at 01:59 AM.

02-07-2011, 02:46 AM	#2
ffinkernagel Senior Member 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.

02-07-2011, 03:58 AM	#3
khb Member Location: Oslo Join Date: Dec 2010 Posts: 15	Of course. Thanks

08-14-2011, 11:40 AM	#4
rossignol Junior Member Location: Finland Join Date: Aug 2011 Posts: 1	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.