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
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)
Disclosure: Cross-posted to Bioconductor support