About ATAC-seq call peak (hmmratac) and differential analysis via MACS3

[DayTimeMouse]

Discussed in #675

^{Originally posted by DayTimeMouse November 19, 2024}
Hi，

Thanks for developing this function to call peaks for ATAC-Seq.

I ran macs3 hmmratac -i final.bam -n treat --cutoff-analysis-only. Then, I got the report(see the attachment), according to the document, -l may set to 45 (that can capture moderate number ( about 10k ) of peaks with normal width ( average length 500-1000bps long)), but I'm confused about setting -u and -c parameter.
The report:
treat_cutoff_analysis.txt

Another question, I have control and treatment, which are no repeats. So, can I use MASC3 to do differential analysis? Could you give me a detail approach？

Thanks in advance.