How to identify viral transcripts from an RNAseq library of an infected cell?

Question

[j.thomas93]

Hi all,

Something of a newbie to bioinformatics hoping for some help! I extracted RNA from an HIV-1 infected cell and sequenced the whole transcriptome using MinION with oligoDT primers, so have both cellular and HIV transcripts (presence of HIV transcripts in the library are confirmed by Kraken2 and mapping to a HIV genome).

My plan was measure the relative abundance of each HIV transcript type in the cell (with the view to compare this in different cells later down the line). But I have no idea how to do this really. So i basically want to map the reads to the HIV genome and then somehow measure the abundance of each transcript variant (so like a transcript that would encode env, rev etc). What would be the best way to do this?

Thanks in advance for any help!

JT

[GenoMax]

Take a look at virdetect (paper link). Software is available here.

[j.thomas93]

Thanks for the reply! I will take a look and let you know how i get on

[GenoMax]

Another option could be to use salmon. There is a protocol published here. Make sure you use a long read aligner like minimap2 when you do the alignments.