How to create count file from fastq files

Question

[bioinformatics.girl]

I'm trying to perform a scATAC-seq analysis and have had issues generating a count files from .fastq files. The goal is to generate Count files in order to feed those into a CellRanger pipeline in order to get fragments.

Thank you.

Answer 1

[GenoMax]

If you are interested in staying within cellranger workflow then simply use cellranger-atac count: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/using/count