How to create count file from fastq files
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.
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GenoMax
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bioinformatics.girl •
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bioinformatics.girl •
1 answer
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
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