What is ERVmap?
ERVmap is one part curated database of human ERV loci and one part a bioinformatics tool to allow users to easily determine which ERVs are transcribed in their RNA seq data. The database is curated from the literature and will continue to be updated as investigators identify new ERV loci. The bioinformatics tool contains a unique mapping method that we have developed to account for the highly repetitive nature of ERVs. Our pipeline incorporates our database, is highly stringent to allow very little mismatches between the sequencing reads and the reference, accounts for different read length, and is normalized based on differential gene expression. The details of our pipeline can be found here (Tokuyama M. et al. PNAS 2018). For those of you who have your own computational capacity, the entire codebase is in GitHub (https://mtokuyama.github.io/ERVmap/).
All you have to do is upload your RNAseq data and you will receive raw analysis data in counts.