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single-cell-genetics / vireo

Demultiplexing pooled scRNA-seq data with or without genotype reference
https://vireoSNP.readthedocs.io
Apache License 2.0
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Clarifying the workflow using bulk RNA-seq data for genotyping #38

Open lucygarner opened 2 years ago

lucygarner commented 2 years ago

Hi,

I have bulk RNA-seq data for each of my human samples, plus the scRNA-seq data that I would like to demultiplex with Vireo. Could I just clarify the workflow?

  1. Genotype bulk RNA-seq samples at a list of given SNPs using cellSNP mode 1b. Would you recommend this VCF file: http://ufpr.dl.sourceforge.net/project/cellsnp/SNPlist/genome1K.phase3.SNP_AF5e2.chr1toX.hg38.vcf.gz from https://sourceforge.net/projects/cellsnp/files/SNPlist/?

  2. Run Vireo in the mode "with genotype for all samples" - vireo -c $CELL_DATA -d $DONOR_GT_FILE -o $OUT_DIR In this case the "cell_data" would come from the output of cellSNP.

Is this correct or am I missing any steps?

Best wishes, Lucy

huangyh09 commented 2 years ago

Hi Lucy, Yes, I would also recommend this strategy.

Yuanhua