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single-cell-genetics / cellSNP

Pileup biallelic SNPs from single-cell and bulk RNA-seq data
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Adapting cellSNP for gene-of-interest / indels / multiple scRNA-seq samples #36

Open ychenab opened 1 year ago

ychenab commented 1 year ago

Hi Yuanhua,

I have three suggestions/questions about cellSNP and cellsnp-lite:

  1. Would you consider using the "start" and "stop" parameters in pysam.pileup to allow users to achieve faster SNP detection within a region/gene of interest?

  2. One of my gene of interest is known to be frequently disrupted by frameshift mutations / indels, but cellSNP only support single-nucleotide variant detection. Could the pipeline be modified to consider indels?

  3. Is it possible to input two or multiple scRNA-seq samples and identify sites that are different across samples?

Thank you!

Best regards, Yiyun