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statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq
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Different Genotype arrays for demultiplexing samples #96

Open carolynmcgrail opened 1 year ago

carolynmcgrail commented 1 year ago

Hello,

We have samples that will be genotyped on different arrays, will this be a problem when demultiplexing due to less overlap of shared snps?

Thank you, Carolyn

hyunminkang commented 1 year ago

I think so. I would recommend imputing the genotypes and extract high-quality (e.g. RSQ > 0.9) imputed genotypes in such cases.

Thanks, Hyun.

Hyun Min Kang, Ph.D. Professor of Biostatistics University of Michigan, Ann Arbor Email : @.***

On Wed, Oct 5, 2022 at 1:23 PM carolynmcgrail @.***> wrote:

Hello,

We have samples that will be genotyped on different arrays, will this be a problem when demultiplexing due to less overlap of shared snps?

Thank you, Carolyn

— Reply to this email directly, view it on GitHub https://github.com/statgen/demuxlet/issues/96, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABPY5OIQIVOSS6HFY6LIAVTWBW2QVANCNFSM6AAAAAAQ5YF6E4 . You are receiving this because you are subscribed to this thread.Message ID: @.***>