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Published 20 hours ago • verified publisher icon statgen

using demuxlet for two mouse strain ( BL6 and BALBC)

Open yxian9 opened this issue 6 years ago • 4 comments

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!

yxian9 avatar Feb 03 '19 01:02 yxian9

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

chenv3 avatar Oct 24 '22 19:10 chenv3

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

hyunminkang avatar Oct 24 '22 20:10 hyunminkang

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?

chenv3 avatar Oct 24 '22 21:10 chenv3

Sure, you can do that.

hyunminkang avatar Oct 24 '22 22:10 hyunminkang