Adding broad peak calling option in MACS3 function?

kaizhang / SnapATAC2

Single-cell epigenomics analysis tools

https://kzhang.org/SnapATAC2/

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Adding broad peak calling option in MACS3 function? #210

Open zkcao opened 10 months ago

zkcao commented 10 months ago

Hi Kai,

First of all, thank you for developing snapATAC2!

I was wondering if we could have the option to call broad peak when using macs3. I see that it's currently not supported.

Thank you! Zhenkun

kaizhang commented 10 months ago

Thanks for this suggestion! I'd like to add this feature. But broad peak calling is harder than narrow peak calling. I need to spend some time to test different options. Please feel free to make any suggestion about the broad peak calling workflow. For the time being, you can export the cluster level fragment file using ex.export_fragments and call peaks by yourself.