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?
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.
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?
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/?
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