Closed cnk113 closed 3 years ago
Actually, I believe scATAC-seq reads are paired-end and only require genomic alignment. It would be challenging to modify scSNV to work with this type of data. You could probably align the reads with BWA-mem if you want similar alignment results. I will look into modifying the pileup command to work with scATAC-seq data.
Yeah cellranger-atac already uses BWA-mem internally, and marks duplicates per cell so hopefully won't be too problematic.
Thanks, Chang
Apologies, it will take too much time to modify my pileup program to work with scATAC-seq data at this moment. Perhaps there are other methods already available that will work with scATAC-seq / whole genome data. Perhaps tools designed to work with 10X single cell CNV data etc.
Hello,
I read your paper, and I was wondering if it was possible to do this with scATAC-seq where the reads are pos de-duplicated per cell? I'd assume the genome coverage would be much higher in scATAC-seq and therefore easier to detect SNV.
Thanks, Chang