How to peak calling

[koh2ng0]

Hi,

First of all, thank you for sharing a wonderful dataset and study of scATAC-seq. I took your dataset and analyzed scATAC-seq data according to the method of your manuscript. However, I don't know well how to peak calling using ArchR. So, Could you explain the way of peak calling processes with parameters in more detailedly?

Sincerely,
Koh

[Biocard]

@koh2ng0
Hi,how were you able to obtain the Fragment file? Did you run the cellranger pipeline after downloading the original data?

[smorabit]

Hi, you can read more about peak calling with ArchR at this page.

[koh2ng0]

@Biocard

Hi, I obtained fragment files from https://www.synapse.org/#!Synapse:syn22079621/. Thanks.