generating VCF for REGION_VCF from RNA-seq data

single-cell-genetics / cellSNP

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

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generating VCF for REGION_VCF from RNA-seq data #35

Open gebdu opened 1 year ago

gebdu commented 1 year ago

Hi,

This is more naive question as I do not have experience in SNPs.

I have 2 cell-lines scRNAseq data, combined sequenced. Now would like to separate using cellSNP (& vireo). I got bulk RNA-seq data for this 2 cell-lines. So, question is how to make VCF file for REGION_VCF option?

thanks,

hxj5 commented 1 year ago

Hi, you may call SNPs from (merged) bulk RNA-seq data to generate the VCF for REGION_VCF option, e.g., with samtools or cellsnp-lite mode 2b, and then pileup the scRNA-seq data with the VCF file.