While going through the Analysis of Chip-Seq data tutorial, I realized that one of my input controls has significantly less sequencing coverage (fingerprint plot link - https://imgur.com/a/y8yXo) than its experimental counterpart. The control sample has 1/4 the mapped reads of the treated sample (4 million vs 16 million). My concerns are as follows:
In spite of the shallow coverage, is the control sample still usable? I would think it has some value but I am not sure if I am missing something.
MACS documentation mentions that the inclusion of a control sample is optional but I have not been able to definitively determine the impact of not using a control on the results. It would seem that the use of the control would help to limit false positives. Is that accurate?
With or without a control sample, wouldn't visualization of the sample BAM files and called peaks be an adequate way to validate the accuracy of MACS2?
Thanks for the help!!