ChIPQC read depth doesn't match BAM files

Question

[bertb]

Hello,

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?

Thanks,

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")

Answer 1

[Rory Stark]

Which part of the report do you see the lower number of reads? By default, ChIPQC only checks a subset of the reads (those mapping to the first chromosome on which there is a peak) for its QC metrics rather than processing all of the reads. Generally, this runs much more quickly and gives indicative results.