A way to detect nonsense mutations in RNA-Seq data

Question

[cpm186]

Hi,

I am investigating a protein involved in Nonsense mediated mRNA decay. I overexpressed the protein in cells and conducted RNA seq on the lysate. I was wondering if there is a way to analyze RNA seq data to look for nonsense mutations specifically. Since these transcripts are normally degraded via NMD, I want to see if there is an increased accumulation of nonsense transcripts when NMD is dysregulated.

Thanks!

Answer 1

[Sean Davis]

You could perform variant calling on your RNA-seq data (or, ideally, on exome sequencing from the cell line) and then identify the various variants from there using tools like Annovar, SnpEFF, or VEP.