Is it possible to check a specific gene level in a specific genus?

Hello. I always thanks for your help.

I want to check a specific gene level in a specific genus.
Is it possible with QIIME2-Shotgun distribution?
If possible, how can I do it?

I'm sorry if this may be a topic that overlaps with the posts I've posted so far.

Thank you for your help!

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Hello @sooni,

Could you explain what you mean by gene level?

A specific gene level means gene expression level of a specific gene.

Hello @sooni,

Are you working with RNA sequences?

Yes. I am working with RNA sequences. Exactly, I am working with shotgun sequencing data.

Hello @sooni,

I believe you can still import your RNA sequencing data as dna sequences in the typical fashion (see the importing docs for more information).

Then, if you want to do targeted analysis you could use dada2 or qiime vsearch dereplicate, then qiime vsearch cluster-features-closed-reference with your genes of interest.

Or, if you want to do gene discovery you could use qiime assembly assemble-meaghit -> qiime moshpit eggnog* in the shotgun distribution.

Please note that I am not very familiar with RNA sequencing data and the above is just a rough suggestion. Please also note that the functionality in the shotgun distribution is still in an alpha state and not fully documented yet.

Thanks for your reply.
If I come across something I don't know during the analysis, can I ask more?

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Hi @sooni,
You are always welcome to ask more questions as your work through the analysis. If its a follow-up question feel free to post on this thread, but if its a different isssue make sure to make a new topic!

Hope to see you around the :qiime2: forum soon!

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