I'm new in bioinformatics in general, and I try to do ChIP-seq analysis.
I used Macs2 for peaks detection for two samples- treatment and control. The command line was identical, but when I looked at the peaks at the UCSC, two problems were revealed:
macs2 recognized the treatment peaks as longer peaks systemically. When there is one long treatment peak, there are few short control peaks, even when it looked the same at the IP and input levels.
many times macs2 found peak only in the treatment even though the IP looked similarly and the input was clean.
Do you know what the problem could be? Or direct me to the right parameters that could be connected to it?
I appreciate the help, Nehora.