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

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.

ADD COMMENTlink modified 3 days ago by Rory Stark1.7k • written 6 days ago by kennethcondon200710
0
gravatar for Rory Stark
3 days ago by
Rory Stark1.7k
CRUK, Cambridge, UK
Rory Stark1.7k wrote:

Let's consolidate discussion of this issue here:

DiffBind for ATAC-seq

 

ADD COMMENTlink written 3 days ago by Rory Stark1.7k
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