Unable to import my files as .qza

[isabelle_miserani]

I have a R1 and R2 reads as a fastqsanger, and I need to run a taxonomic analysis of the sequencing results. The 2 files are in Galaxy, but every time I use the tool to import into qiime2 artifact, it gives me a message, “No list data set collections available”.

I also have a data set with all the different reads that are already demultiplexed, and the same message appears every time.

What should I do to be able to get my files to become a .qza?

[jennaj]

Welcome @isabelle_miserani

For this analysis, you could use the tools directly if you want to. Some potential tutorials for follow are here → Galaxy Training!. If you had a tool in mind, check the form since more tutorials will be linked there, plus you can search that site directly. This would avoid the need to create the artifacts.

However, if you still want to use the Qiime/Qiime2 tools instead, you can get your artifact organized by putting the data into a collection. The reads will need to have the original sequencing identifiers. Then you input to the import tool, and proceed to downstream tools.

This topic here has the links to the resources we have:

@jennaj

This is one of them → qiime2 tools import

Others can be found under qiime2_core__tools__import and qiime2

This tool does not have a Galaxy tutorial. Everything is in the original tool documentation, then on the Galaxy forms. Some of the Galaxy help is up in the form where the options are made and some is down in the Help section where you’ll also find the link to the external docs.

To inspect artifacts, you will need to download the file then upload to the site hosted by the original authors. This is another good topic since one of the authors was helping.

@colinbrislawn

As another option, you can download the .qza and .qzv files and view them with
https://view.qiime2.org/

Hope this helps to get you started, and we can follow up more!

[isabelle_miserani]

I am new to this computational approach. So when you say to put the data into a collection, should I create a collection of paired ends? One more question, when you say original sequencing identifiers, do you mean the reads still multiplexed?

[jennaj]

@isabelle_miserani

should I create a collection of paired ends

Yes. For the collection part, see the tutorials here to learn how to create them. You will want the paired end version for what you are doing.

• Hands-on: Using dataset collections / Using dataset collections / Using Galaxy and Managing your Data

@isabelle_miserani

when you say original sequencing identifiers, do you mean the reads still multiplexed

No, you can have the reads separated into sample groups. I’m referring to the sequence identifiers on the @ lines. This is a nice reference guide about how to interpret those.

• Hands-on: NGS data logistics / NGS data logistics / Introduction to Galaxy Analyses

Hope this helps! See the other topics I referenced. One has a walk through of adjusting the sequence identifiers to match the pattern this tool is expecting.