Entering edit mode
10 months ago
bertb ▴ 10
I am using ChIPQC, and the report is listing read depths that are much lower than I can plainly see in the MACS2 output. For instance, one of my BAM files reports ~13 million fragments, but then only ~550,000 reads in the ChIPQC report. Any suggestions as to why this might be happening?
library(ChIPQC) library(SerialParam()) register(SerialParam()) chipObj <- ChIPQC(B) #B is my sample sheet ChIPQCreport(chipObj, reportName="ChIP QC report: Rpb1 ChIPseq broadpeak 3 rep")