Hi, i’m trying to use ChIPseeker to look at my MACS2 called peaks. I aligned my ChIP data using BWA against HG38, used MACS2 to call peaks then ran ChIP seeker with default settings - my annotation source was hg38.refGene.gtf.gz from UCSC. Everything runs fine, but when I load my ChIP coverage data along with the called peak bed file into IGV, the annotations spat out by ChIP seeker dont match the location of my called peak.
For example, there is a peak called (according to IGV) in the 3’UTR of LDLRAD3 (chr11:36231274-36231622), but the feature is then annotated by ChIP seeker as being in the 3’ UTR of COMMD9 (chr11:36272292-36289424). Although neighbouring, it’s the wrong gene and is ~42kb downstream of the MACS called peak. Looking through my data, only 10 or so peaks, shows that this happens approx 50% of the time!
Does anyone have any ideas of what could be going on? Hopefully an annotated screen grab of the IGV gene track will be shown below.
