A way to detect nonsense mutations in RNA-Seq data
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!
1 answer
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.
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