search

GWW / scsnv

scSNV Mapping tool for 10X Single Cell Data
MIT License
22 stars 4 forks source link

Ability to use w/o UMI? #2

Closed cnk113 closed 3 years ago

cnk113 commented 3 years ago

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

GWW commented 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.

cnk113 commented 3 years ago

Yeah cellranger-atac already uses BWA-mem internally, and marks duplicates per cell so hopefully won't be too problematic.

Thanks, Chang

GWW commented 3 years ago

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.