Genetic variation calling (SNPs) from bulk RNA-seq dataset
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6 weeks ago
Shicheng Guo ★ 8.8k

Dear All,

Is there anything should be careful for the workflow developed for Genetic variation calling (SNPs) from bulk RNA-seq dataset. Is there mature established workflow for SNP identification from RNA-seq data?

Thanks.

RNAseq SNP • 189 views
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6 weeks ago

I believe that DNA based variant callers suffice, for a review see the following paper:

RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species, Frontiers of Genetics, 2021

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8273700/

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