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statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq
Apache License 2.0
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using demuxlet for two mouse strain ( BL6 and BALBC) #35

Open yxian9 opened 5 years ago

yxian9 commented 5 years ago

Hi,

Demuxlet is a awesome tool! I'm wondering can I use it to demuplex scRNA experiment mixed with mouse cell from BL6 and BALBC strain? If it works, how should I handle the VCF file? In this case, BL6 will be the reference genome, and I only have one VCF file for BALBC strain. Can Demuxlet work with VCF file containing only one sample variation information?

Thank you very much!

chenv3 commented 1 year ago

Hi,

I was wondering if there was ever any resolution to this question, or how to handle this sort of situation? I've also run into a situation where we need to do the same thing.

Thank you

hyunminkang commented 1 year ago

demuxlet requires genetically distinct samples, so you always need VCF that contains multiple individuals.

chenv3 commented 1 year ago

Thank you for the response. I was wondering if we could just have two individuals in the vcf file with one for BALBC and the other individual just having all entries matching the reference?

hyunminkang commented 1 year ago

Sure, you can do that.