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NarrowPeak format -Peak field

Hi , In Narrow (or Point-Source) Peaks format there is a field called "peak" that is described : peak - Point-source called for this peak; 0-based offset from chromStart. Use -1 if no point-source called.

can anyone explain it more please? does it represent the based offset from nearest peak ?

chip-seq dnase-seq bed
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updated by ATpoint ATpoint • written by kimkes25 • kimkes25

1 answer

This is the so-called peak summit, so the part of the peak with the highest count. Say you have a peak interval like

chr1     1      100

and the value for this field would be 50 then you would add 50 to the start coordinate so 1+50 to get the position of the summit which would be 51 on chr1. Summits only make sense for sharp histone marks or transcription factors.

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written by ATpoint ATpoint

so if I look at the BED format and I have : 

bin chrom   chromStart  chromEnd    name    score   strand  signalValue pValue  qValue  peak
590 chr1             713835          714424          chr1.1 1000                       0.1621            10.6     -1            253

so if there are several peaks in the interval between 713835 - 714424 ,the highest count is at position 713835+253 ?

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updated by ATpoint ATpoint • written by kimkes25 • kimkes25

It depends on the peak caller how peaks are reported. I cannot comment on your general statement.

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written by ATpoint ATpoint

Hi ATpoint - quick question. In my mind, 0-based means counting from 0. So if the peak value column shows 50, the summit is 52 (1 + 51), not 51 (1 + 50). Please correct me if I am wrong.

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written by aaronlogsdon2001 • aaronlogsdon2001

I do not follow, can you please add a chr-start-end example.

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written by ATpoint ATpoint

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