Question: Wrong coordinates of peaks in DiffBind
0
gravatar for grant.hovhannisyan
21 months ago by
grant.hovhannisyan2.0k wrote:

Hi All,

I'm analyzing ATAC-seq data and use MACS2 for peak calling and DiffBind for occupancy and affinity analysis.

In occupancy analysis when I try to find peaks that are unique to one group, it seems that DiffBind confuses the contigs and coordinates of the peaks. For example I get,

SU68  390602  392045  1444      * 2.191028e-03
SU39  136859  137210   352      * 2.175033e-03
SU79  564195  565710  1516      * 2.161226e-03

but contigs SU68, SU 39 and SU79 in reality are very short (ca 1kb each), so it is not possible that peaks are located at the coordinates that DiffBind displays.

MACS2 output files seem fine, so I guess this is either a bug in DiffBind or it somehow changes the coordinates of chromosomes. Any ideas?

Here is my code after loading the peaks:

dba.overlap(SU_vs_hybrid, SU_vs_hybrid$masks$Parent, mode = DBA_OLAP_RATE)
dba.overlap(SU_vs_hybrid, SU_vs_hybrid$masks$Hybrid, mode = DBA_OLAP_RATE)


SU_vs_hybrid_unique<-dba.peakset(SU_vs_hybrid, consensus = DBA_CONDITION,minOverlap = 0.33)


SU_vs_hybrid.OL<-dba.overlap(SU_vs_hybrid_unique,SU_vs_hybrid_unique$masks$Consensus)
only_parent_peaks<-as.data.frame(SU_vs_hybrid.OL$onlyA)

Thanks

Disclosure: Cross-posted to Bioconductor support

diffbind atacseq • 712 views
ADD COMMENTlink modified 21 months ago • written 21 months ago by grant.hovhannisyan2.0k

Has anybody experienced the same?

ADD REPLYlink written 21 months ago by grant.hovhannisyan2.0k

Hi. I am having this issue with my ChIP-seq data which used MACS2 and then DiffBind. Did you figure out the issue? I tried the suggestion from Rory Stark of explicitly setting the data type to data frame but the issue persists.

ADD REPLYlink written 5 months ago by aboyd0030

Hi, no I did not find a solution unfortunately. The suggestion of Rory Stark also did not fix it.

ADD REPLYlink written 5 months ago by grant.hovhannisyan2.0k

Thank you for your reply. I'm going to try the HMM based THOR program then.

ADD REPLYlink written 5 months ago by aboyd0030
1
gravatar for grant.hovhannisyan
21 months ago by
grant.hovhannisyan2.0k wrote:

Rory Stark, the developer of DiffBind answered the question in Bioconductor Support.

ADD COMMENTlink written 21 months ago by grant.hovhannisyan2.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1069 users visited in the last hour