fragments.tsv.gz file in ATAC seq

Question

[Chris]

Hi all,

I looked at some tutorials ATAC seq. They use fragments.tsv.gz at the beginning of the analysis. For my ATAC seq data, I have fastq, bam and bw files but not fragment file. So the fragments files will be created from fastq files, is that correct? Thank you so much.

Update: I think I figured it out.

[tingting]

Are you referring to fragments.tsv.gz? it was created from cellranger atac count, see from this link:

https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/using/count#header