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statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq
Apache License 2.0
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Naive question about VCF file #25

Open NicolasHipp opened 6 years ago

NicolasHipp commented 6 years ago

Hi everyone,

Maybe a big naive question, but do you think that it is possible to generate the vcf file necessary for demultiplexing based on RNAseq bulk for each patient?

Thanks a lot, nicolas

hyunminkang commented 6 years ago

Hi Nicolas,

We are working on a version of demuxlet that does not require external genotypes. We will hopefully have an update soon so that you do not need bulk sequencing :)

Hyun.

On Tue, May 29, 2018, 9:48 PM NicolasHipp notifications@github.com wrote:

Hi everyone,

Maybe a big naive question, but do you think that it is possible to generate the vcf file necessary for demultiplexing based on RNAseq bulk for each patient?

Thanks a lot, nicolas

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NicolasHipp commented 6 years ago

Woo can't wait to see that :D!!!!. Do you think that the update will be release before summer? (I anticipate my supervisor's question :p)

Thanks for the work! Nicolas

x811zou commented 6 years ago

Hi! I also have a question about the .vcf file. In your tutorial, how did you make the vcf file? Was it made from the only bam file from 10X 50%:50% Jurkat:293T Cell Mixture? Will it contain the genotype info for mixed samples?

Previously I thought we have to obtain the vcf file by using single-cell rna-seq from all individual samples. (e.g. Monovar) But that makes using demuxlet meaningless because we already have sample info. Pleae forgive my naive questions!

bio-la commented 6 years ago

@hyunminkang Hi, can you please give more details on how exactly this should work? Can't wait to see it in action.

achamess commented 6 years ago

Hi @hyunminkang. That sounds great. I hope to see it soon. Re @NicolasHipp 's question, is it advisable to use bulk RNA-seq to generate the VCF file with SNPs?

bio-la commented 6 years ago

Hi @achamess , i used bulk rnaseq (3' sequencing) and followed GATK pipelines to do variant calling on RNASEQ. with the same parameters (I tested multiple alpha and geno-error) I have better results (read: more SNG than AMB/ DBL) with the RNAseq-VCF than the array.

bio-la commented 6 years ago

hey @hyunminkang , any update on the version of demuxlet that does not require external genotypes?

thanks!

maximilianh commented 5 years ago

hey @hyunminkang, this is really cool, any updates on this?