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statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq
Apache License 2.0
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VCF file to reproduce "Multiplexing droplet-based single cell RNA-sequencing using natural genetic barcodes" analysis. #5

Closed SebastienNin closed 6 years ago

SebastienNin commented 6 years ago

Hello, I'm Sébastien Nin, currently working in the Centre d'Immunologie de Marseille Luminy in France. I would like to use demuxlet to enable the multiplexing of single-cell RNA-seq samples. In order to do this, I did the tutorial and I found it very good built. To continue my practice with this tool, I would like to reproduce the analysis that can be found in the paper "Multiplexing droplet-based single cell RNA-sequencing using natural genetic barcodes". I already found the bam files on GEO but I can't find the vcf file you used. Can you advise me on the way I can get the vcf file?

Have a nice day, Best regards,

Sébastien

yimmieg commented 6 years ago

in order to keep this repo small, we put the vcf for reproducing the results in the paper here:

https://github.com/yelabucsf/demuxlet_paper_code/tree/master/fig2