NBCI-taxonomic analysis

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1

Hi,

I have a quick question, I have performed all of my analysis in qiime2, but I had forgotten to check my rep-seq.qzv against blast. My question is, when I attempt to load the .qzv file, I get an error stating, Query string appears to contain illegal entries (e.g. links to web pages). I am therefore not sure how to get NCBI to read the file. I did notice that we can click on the qzv file taxon and it takes us directly to the NCBI website.

Thanks again

2

Hello Fabiola,

In order to do a blast search online, you need to extract your sequences.fasta file from inside your .qva Qiime artifact. You can read more about extracting here. The basic command will be something like:

qiime tools extract \
  rep-seq.qza \
  --output-dir extracted-rep-seqs

Let me know if that helps,
Colin

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Oh, I completely misunderstood the message on the tutorial. I literally thought I could use that file directly in to NCBI website.

Thanks again :slight_smile:

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I wish the NCBI website accepted .qza files directly. They could, but I don't think they do right now.

BTW what line of the tutorial was confusing? We should change that so that is doesn't confuse other people.

Colin

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5

Thanks, It worked!

Maybe it was just me, but this is the portion of the tutorial that I misinterpreted.
#It is after creating the taxonomy.qza

"Recall that our rep-seqs.qzv visualization allows you to easily BLAST the sequence associated with each feature against the NCBI nt database."

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Oh I recognize that line! Here is what that means:

When you use Q2-view to view your rep-seqs.qzv (link to example file), it lists the feature ID and full DNA sequence. When you click on the DNA sequence, it automatically takes you to the NCBI Blast website so you can do a search for that read.

Does that make sense?

I sounds like you would like to do a blast search for all of your reads, which is why I recommended extracting your rep-seqs.qza file.

Colin

P.S. How could we make that specific line more clear? Could we clarify which file or use, or maybe how to get files onto the NCBI website?

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7

Ah, okay, that makes sense. I did notice that I could click on each sequence individually, after not being able to upload the .qzv file, but I didn't realize that, that was what that comment meant.

Thank you for your recommendation, that saved me a lot of time.

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