Entering edit mode
5 months ago
pixie@bioinfo
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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.
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.
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.
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.