Hey guys, I am working on ChIP-Seq analysis using MACS and annotation of peaks using Homer. I have 2 different IgG ChIP-seq control sequences which give me different sets and numbers of peaks using MACS. I was wondering if there is a way to check the quality of reads or sam files to be able to choose 1. I have tried FASTQC for sequence quality scores and samstat for qualilty of sam files and both the files pass the criteria. What would be the best way to pick 1? Thank you for your help!
Most peak callers expect the control sample to represent the actual genomic background (e.g. input). So, though you can use it, the IgG-only control is not recommended for use as a control samples in ChIP-Seq peak call analyses as they don't actually represent the true genomic background for that sample, unlike using an input DNA control. IgG-only controls are useful for assessing whether there was potential non-specific carryover, e.g. DNA binding non-specifically to IgG. Also, the concentrations of DNA from those samples are (if performed correctly) significantly lower than IP or input.
We normally recommend using them in screening samples pre-sequencing as a control, e.g. assessing samples via QPCR, but we don't recommend sequencing them anymore.
EDIT: I should add, some callers do allow for IgG but I would certainly look at the documentation for the tool. You can certainly run the samples w/o any control as well.