SNP Analysis on Single Cell Data from 10x

Question

[rohanverma2.2017]

Hello,

I want to figure out how I can identify SNP's in a single-cell RNA-sequencing run produced by the 10x Genomics Chromium Single Cell 3' Solution. I want to essentially cluster cells into groups by their SNPs to see if differences can be detected in donor versus host cells. What is the best way to go about this process and is there anywhere I can find an established workflow for this?

I wanted to do something similar to snpclust: https://github.com/10XGenomics/single-cell-3prime-snp-clustering but it seems like it is not supported.

Any help would be appreciated.

Thank you in advance!

[droseeee]

Hi,

I am attempting to do the same. Has anyone figured out a method with R?

Thanks!!

[ahmedakhokhar]

Try to check it out! https://www.scrna-tools.org

Answer 1

[Kevin Blighe]

Hey,

Please be aware of the limitations of calling variants from RNA-seq data: A: Inferring genotype based on RNA sequnces

The GitHub page to which you linked us is the home-page of 10x itself (on GitHub). Please contact them directly about how to best perform what you aim to do. E-mail is right there: https://github.com/10XGenomics

Kevin

[igor]

For single-cell sequencing, you may actually be better off with RNA than DNA. For DNA, you are starting with only 2 copies (not accounting for CNVs), so your true coverage is really 2x at best. At least with RNA, you may have many more molecules that you starting with.