Hi,

Recently I'm working on RNA-seq data from pigs, and I want to: 1. get all porcine endogenous retroviruses (PERV) loci in pig genome (then I can visulize the reads of these regions) 2. quantify PERV

I don't know where to start. There are so many sequences in NCBI's nucleotide database: https://www.ncbi.nlm.nih.gov/nuccore/?term=(PERV)+AND+%22Sus+scrofa%22%5Bporgn%3A__txid9823%5D. Or should I start with sequences of here: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=61673.

I've read a similar thread: Endogenous Retrovirus Expression from RNA-Seq, but still don't know how to do.

Thanks!