Yes Sonja, the best sub window is a rescan of the enriched region to
identify the highest scoring 50bp window. You can also take the center of
the best window. -cheers, D
On 11/18/10 4:28 AM, "Sonja Althammer" <son...@go...>
wrote:
> Hello!
>
> I have been looking at the output files of the ChipSeq applications and I
> couldnt find a summit position (= maximal pileup of reads). Also as it is a
> window approach I guess there is no such thing? Would it be correct then to
> use the center of the best sub windows in the corresponding gff file? BTW are
> these also sorted according to the significance of a peak?
> I want to look for motifs in the 100bp region underlying the summit of peaks,
> that's why I need this position of reference....
>
> Thanks in advance!
> Sonja
>
>
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