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single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
131 stars 11 forks source link

cellsnp-lite on other species, organism #134

Closed dongwankimlab closed 2 months ago

dongwankimlab commented 2 months ago

Hi, thank you for nice software. I have a quick question.

Would it be possible to try cellsnp-lite on 10x scRNA-seq & Illumina bulk RNA-seq data from diploid chimpanzee sample?

Thank you in advance.

hxj5 commented 2 months ago

Hi, generally speaking, the answer is yes. If you have a list of (common) SNPs at hand, you may run mode 1 (mode 1a for 10x scRNA-seq data and 1b for bulk data), otherwise, you may run mode 2 to genotype whole chromosomes (mode 2a for 10x data and 2b for bulk data; and set proper --chrom option). For detailed instructions on each mode, you may check out the section Quick Usage in the manual.

dongwankimlab commented 2 months ago

Thank you very much. I'll try!