Question: Using Diffbind on ATAC data - adapter offset issue
gravatar for kennethcondon2007
11 months ago by
kennethcondon200710 wrote:



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.




ADD COMMENTlink modified 11 months ago by Rory Stark2.3k • written 11 months ago by kennethcondon200710
gravatar for Rory Stark
11 months ago by
Rory Stark2.3k
CRUK, Cambridge, UK
Rory Stark2.3k wrote:

Let's consolidate discussion of this issue here:

DiffBind for ATAC-seq


ADD COMMENTlink written 11 months ago by Rory Stark2.3k
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