Using Diffbind on ATAC data - adapter offset issue
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YaGalbi ▴ 20
@yagalbi-11519
Last seen 2.0 years ago
MRC Harwell Institute, Oxford, UK

Hi,

 

I'd like to use Diffbind on Atac data. However what is done about the adapter adjustment that occurs before peak calling? For peak calling all forward reads are offset by +4 bases and reverse reads by -5 so aligning peak positons to BAM file positions of the reads may need reversing of the offset.

Forward strand example

Position:     1   2   3   4   5   6   7   8   9   10 

Base:          A   G   A   T  A   C  C   A   A    T

BAM read:        G--------------C                                                  Aligner places G---C read at positions 2 to 6

Peak:                                   6----------------10                           Peak calling after offset calls a peak at 6-10

 

Does anyone have experience with this? Am I thinking correctly? It should be a simple fix, I'm just wondering if I am thinking correctly and this is needed.

 

Thanks,

Kenneth.

Diffbind Atac adapters • 987 views
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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 23 days ago
CRUK, Cambridge, UK

Let's consolidate discussion of this issue here:

DiffBind for ATAC-seq

 

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