Deletions, Translocations And Cnv From Rna-Seq

Question

[kanwarjag]

Is it possible to find out deletions tarnslocations and / or copy number variations between RNA-seq data of control vs treated samples. The data is PE with enough coverage ( say around 30X).

Thanks

[Devon Ryan]

In the title you mention RNA-seq, but in the body you mentioned exome data. Which of the two are you doing?

[kanwarjag]

I edited my post to RNA-seq

Answer 1

[Chris Miller]

You can absolutely find translocations, as long as they involve the fusion of two gene products. These will be a small percentage of the total SV events in the genome. Chimerascan is one of many tools for doing this sort of thing.

You will not be able to detect copy number events, with the possible exception of very small deletions that fall entirely within an exon. Consider this: if you see more transcripts from a particular gene in your RNAseq data, is it overexpressed, copy-number amplified, or both? There's really no way to tell without corresponding evidence from the genomic DNA.