Can we use Qiime 2 for RNA seq of mycoviruses?

[Sidha (Ponsidha HIn)]

Dear Sir,

Can anyone tell me about the Usage of Qiime 2 for analysis of RNA seq of Mycoviruses? I have got the attached files from the company. Could anyone see and help me? If this can be analyzed with the Qiime 2, which step should I take to begin?

Thanks

[colinbrislawn (Colin J Brislawn)]

Good afternoon @Sidha,

Thank you for posting on the forums. Are you sequencing the metatranscriptome of Mycoviruses, or are you targeting a marker gene using PCR? Is your data targeted or shotgun sequencing?

Qiime 2 is best for certain types of data, so I would like to know more about the data you have.

Thank you,
Colin

[Sidha (Ponsidha HIn)]

Sir,
Thanks for your reply. I have extracted Total RNA from a fungus and then we sent the Total RNA samples for RNA seq to the company. The company sent us sequences and when we do blast manually we get the mycoviruses.

Regards,

[colinbrislawn (Colin J Brislawn)]

Hello @Sidha,

Ah OK!

Because you have total RNA (and not just a gene targeted with PCR), I'm not sure the standard Qiime 2 workflow will be the best option.

Let's see what the Qiime devs recommend!

Colin

[jbisanz (Jordan Bisanz)]

Hi @Sidha,
What were the original questions you wanted to ask with your dataset, and what are the questions you want to ask now? Ex: what proportion of total RNA is viral, and what viral families are present? Is there a reference genome for your fungus of interest? When you say you blasted the sequence, was that raw reads, or the trinity assemblies of the transcripts?
Jordan

[Sidha (Ponsidha HIn)]

Thanks. I want to ask whether qiime 2 can be use for RNA seq data like mycoviruses. May be we cannot use. Like for the marker genes, ITS or 16S we normally use qiime 2. What about RNA seq data? This was my question.

[Nicholas_Bokulich]

Hi @Sidha,
We do not yet have any established pipelines for RNAseq data in QIIME 2, though we hope to build the capacity in the future.

You could check out q2-metaphlan and q2-shogun to see if these help. These are community-developed plugins for shotgun metagenome sequencing, but might be used for metatranscriptome data too. I am not sure but please let us know what you find!