How to quantify the viral sequencing reads from RNA-seq data?
1
0
Entering edit mode
4 months ago
Huy Duong • 0

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!

RNA-seq viral alignments quantification reads • 254 views
ADD COMMENT
1
Entering edit mode
4 months ago

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1914 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6