Questions on entry point to make snap files from 10x datasets

[shhxiao19]

Hi,

I would like to make snap files from 10x datasets. Based on the snapatac tutorial, https://github.com/r3fang/SnapATAC/wiki/FAQs#10X_snap, there seems to be several ways to do it, e.g., starting with fastq files from cellranger-atac, using the position sorted bam files from CellRanger, and using the fragment.tsv files from CellRanger. I’m wondering which method you would recommend if we want to have more flexibility in getting genomic regions. Thank you for your insight.

Best regards.