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statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq
Apache License 2.0
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version of demuxlet that does not require external genotypes #41

Open bio-la opened 5 years ago

bio-la commented 5 years ago

Hi, about a year ago @hyunminkang mentioned that there would have been an upgrade on the genotyping strategy.

It seems nothing has happened (?)

Has anyone tried genotyping on 10x data to deconvolute individual genotypes from pooled samples, and would something like this tool work? 10.1038/s41467-018-07170-5

Any suggestion is welcome thanks!

maximilianh commented 5 years ago

Also interested in this. I guess we need a reply from @hyunminkang or develop our own strategy...

yimmieg commented 5 years ago

https://github.com/statgen/popscle https://github.com/statgen/popscle

On Apr 26, 2019, at 5:15 AM, Maximilian Haeussler notifications@github.com wrote:

Also interested in this. I guess we need a reply from @hyunminkang https://github.com/hyunminkang or develop our own strategy...

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maximilianh commented 5 years ago

Wow that was a quick reply! many thanks!

bio-la commented 5 years ago

Hi, thanks @yimmieg for the reply. not sure about how helpful it is for others trying to do the same, @maximilianh , but these tools seem to be capable of handling the demultiplexing without input external genotype.

Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants Genotype-free demultiplexing of pooled single-cell RNA-seq Using single nucleotide variations in single-cell RNA-seq to identify subpopulations and genotype-phenotype linkage

you still have to validate at least some of the hits to identify the samples at the end, though, so it's not exactly genotype free, you just do it at a different stage and don't necessarily need the external genotypes as an input. hope this helps.