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kaizhang / SnapATAC2

Single-cell epigenomics analysis tools
https://kzhang.org/SnapATAC2/
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[Question from Beginner] How can I use SnapATAC2 if I don't have BAM file or fragment files? #265

Closed JiehoonKwak closed 4 months ago

JiehoonKwak commented 4 months ago

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 commented 4 months ago

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.