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single-cell-genetics / vireo

Demultiplexing pooled scRNA-seq data with or without genotype reference
https://vireoSNP.readthedocs.io
Apache License 2.0
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Recommended tools for bulk RNA-seq genotyping for mode 2 #14

Closed lmweber closed 4 years ago

lmweber commented 4 years ago

Hi, do you have any recommendations for tools to use for genotyping multiple bulk RNA-seq samples for running in mode 2?

In our dataset, we have several matched bulk and single-cell RNA-seq samples. So far we have been using only the single-cell samples together with the VCF from 1000 Genomes Project, but we would also like to check if we can get improved performance by genotyping the matched bulk samples.

I am fairly new to this, so just want to check if there are any tools you do / do not recommend for the bulk genotyping. Thanks

huangyh09 commented 4 years ago

Hi, it should be a better idea to genotyping the matched bulk samples. You can use bcftools, freebayes or cellSNP mode2, or others.

This benchmarking for single cells can be a useful reference: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1863-4 It treats each cell as a sample, so probably also fits well with bulk RNA-seq.

Yuanhua

lmweber commented 4 years ago

Ok great, thanks! I'll start by trying cellSNP mode 2 (since I am familiar with cellSNP now) or bcftools.

Thanks also for the reference.