ChIP-Seq Quality Control and the RelCC measure
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2.7 years ago
ldyer2006 ▴ 50

Hi all,

I'm currently using the ChIPQC package on a set of bam and peak files generated via bowtie2 and macs2 and then read into ChIPQC via a simple samples sheet. After running the program to examine some of the measures that it calculates, I am a little surprised by a few of the values, and I was hoping that somebody here might be able to explain them to me slightly, as google is not much help.

The following are the metrics from the troublesome .bam file:

         Reads Map% Filt%  Dup% ReadL FragL   RelCC   SSD  RiP%
D_1a   2011555  100     0 69.80    75   300 -181.00 1.350 1.050


I am mostly shocked by the measure here for RelCC and I have read that RelCC is calculated as follows:

RelCC = CrossCoverageScore(max) / CrossCoverageScore(readlength)


As I had understood it, neither of these values can drop below 0. I initially thought that the program was failing to properly calculate the metrics due to the very high level of duplication in this particular sample, but de-duplicating the .bam file and re-submitting leaves me with precisely the same RelCC score of -181.00.

Can anybody lend me a hand in figuring out if this is correct? And if it is correct, what does it mean? Did my lab manage to produce the literal worst ChIP-Seq of all time?

Thanks in advance for any help.

ChIP-Seq Quality Control ChIPQC • 857 views