A method to find if a variant is Genomic or an RNA-Editing variant

Question

[hkarakurt]

Hello everyone, Sorry for my improper title but I could not find a way to explain it better.

As you know variant calling can be applied to RNA-Seq data to identify variants and RNA-Editing events can be identified with this way. But is there a method to predict if a variant is genomic (coming from DNA Sequence) or a possible RNA-Editing event?

Thank you in advance.

Answer 1

[i.sudbery]

No, not really. Not without access to matched DNA-sequencing form the same individual.

SPRINT claims to be able to identify RNA editing sites without the need for matched DNA. But really, this is aimed at identifying sites that definitely are editing, rather than identifying sites that are definitely not (i.e. to clean up SNP calling).

You might think about comapring to a database of known SNP locations (i.e. using the RNA to genotype known SNPs, rather than identifying new ones), or simply excluding all C>T changes from your analysis.