Hi! I'm new to using MACS2 and I would love some help :)
I have a .BAM file from an AF9 ChIP-Seq done with mouse (mm9 genome) cells. I'm trying to find binding sites -500 to +1kb from transcription start sites but I'm not sure how to do this.
Do I need to provide a second file with TSS locations for mm9? How do I even set the parameters for my command to have a start and end point? Is MACS2 even the best software for this task (maybe Homer would better)?
Thank you so much!