How to interpret Per sequence GC content in FastQC for ChIP-seq data?

Question

[Logan]

Hello,

I conducted QC using ChIP-seq data, and among the QC results, I observed that the GC distribution over all sequences in the 'Per sequence GC content' does not follow a normal distribution (showing 3 peaks).

(Inquiries)

1. Is this a common outcome when QCing ChIP-seq data?
2. Why are there three peaks?

Answer 1

[ATpoint]

To be all honest, I never look at these metrics. I check per-base quality and adapter content. I do trimming if there are adapters detected. ChIP-seq is very noisy, this here might be some odd ligation artifacts, leftover adapter dimers that were sequenced or anything else. Much more important is to check alignment percentage, number of callable peaks and percent reads overlapping callable peaks. Also make a bigwig file (for example deeptools bamCoverage) and check peaks on the genome browser/IGV. That is the relevant QC.