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!