Shrimp2 For Rna-Seq

Question

[Mathew Bunj]

I was wondering if I can use SHRIMP2 for RNA-seq alignments of a viral genome? I have not see any paper on this and wonder if I am thinking it rightly or it is mainly used in DNA seq variation analysis?

Answer 1

[JC]

In many cases RNAseq means you need some way to map reads with spliced regions, but for virus, the genes are transcribed in one exon (not true for a few species which have exon-shuffling), so you don't need to split your reads. SHRIMP2 is a general genomic mapper focused principaly on ABI/SOLiD, I think it can work for you as any other mapper.