[Question from Beginner] How can I use SnapATAC2 if I don't have BAM file or fragment files?

[JiehoonKwak]

Thank you for publishing and sharing this excellent module. I've followed some tutorials on GitHub and liked the features.

However, I'm unsure about how to start analyzing data if I don't have BAM or fragment files, especially when I download datasets from GEO.

Thank you!

[kaizhang]

The process of converting FASTQ files to BAM files is dependent on the specific protocol used. It's challenging to create a universal solution that accommodates all platforms.

You can follow the steps outlined in their paper to get aligned BAM files or fragment files.