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!