How to proceed after Kraken2 analysis
0
1
Entering edit mode
3 months ago
pixie@bioinfo ★ 1.5k

Hello,

I am working on tracking and tracing of viruses in plant seed lots. I have total RNAseq data from the seed lots (around 200 samples). I did a kraken2 analysis to fish out certain viruses which we are interested in. For each seed lots, I have the total reads for a given species of viruses. How to I see if for a given seedlot, if there are multiple strains ? I would also like to do the strain level analysis across multiple seedlots. Any idea which tools or what kind of analysis/visualization I could go for ? It can get complicated especially because I have 200 samples.

rnaseq kraken • 403 views
ADD COMMENT
1
Entering edit mode

Do you have a known locus/loci you can target to differentiate known strains? Otherwise, what constitutes different strains vs a polymorphic strain?

If you have enough data to call SNPs in your RNAseq data, you could use a structure barplot to see shared vs. unique diversity among seedlots.

ADD REPLY
0
Entering edit mode

dthorbur Good questions, I will try to think on these lines ! Also, if you know of any metagenomic papers, etc. for reference, I will be excited to have a look.

ADD REPLY
1
Entering edit mode

I've only dabbled in metagenomics, so hopefully someone with more knowledge comes along, but I stumbled across StrainFinder. Whilst it appears they leverage WGS data, some of the principles they applied may be useful.

ADD REPLY

Login before adding your answer.

Traffic: 1113 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