How to quantify the viral sequencing reads from RNA-seq data?

Question

[Huy Duong]

Hi everyone. I'm having problem with quantifying viral reads from my RNA-seq data, which is part of my Final Year Project. Basically, I have filtered the host reads by aligning to host organism genome. The unmapped reads was aligned to viral database with BLASTn, which illustrated the present of some specific virus. Then, I tried to align the unmapped reads to the genome of these virus that I have found using HISAT2, but the output is 0% matched reads. I need some suggestion to solve my problem. Thank you very much!

Answer 1

[Thind amarinder]

There are few tool, which are desined for this purpose such as 'Decontaminer'. take a look here https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2684-x

Here is the Github link for decontaminer tool. https://github.com/amarinderthind/decontaminer

[Huy Duong]

Thank you so much! This article is useful to me.