Proper Way to Import Merged (R1+R2) Data


I got the demultiplexed and merged data (R1 and R2 joined) from one of my collaborators, and wonder which is the correct strategy to import data and start the analysis.

I searched the forum and found people have used the code below to do a similar job,

qiime tools import --type SampleData[JoinedSequencesWithQuality] --input-path pe-joined-manifest.csv --output-path paired-end-2samples

However, I noticed that people also suggested importing data unjoined, and allow DADA2 to do QC.

My questions are:

  • Which strategy should I take to import the merged data? Use the code above or ask for unjoined data.

  • How could I know there is a type called JoinedSequencesWithQuality in the “import” plugin? The tutorial of Importing data¶ does not introduce this type and we do not have a corresponding introduction page on Plugins section for “import”. Could you please tell me where can I find the detailed information for “import” plugin?

Any kind of help would be greatly appreciated!


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Hello Huang,

I think both strategies would work well for data import. Keep in mind that dada2 requires the unjoined data (it uses it during quality control), so if you wanted to use dada2 you have to ask for the unjoined data. If you want to use deblur or vsearch for denoising or clustering, you could import the joined data directly.

I think both strategies would work well and would be highly defensible.

Your second question is very common:

Yeah, why isn’t import listed as a plug-in?

According to the developers, the tools import command is a ‘built-in’ command that’s included with Qiime 2. So because it’s included with Qiime 2, it’s not technically a plug-in. Isn’t that confusing?

But plug-in or built-in, you can run
qiime tools import --show-importable-types and --show-importable-formats
to see all the types and formats currently supported.

Let me know if that helps answer your question!

Happy New Year! :clinking_glasses:

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That is a wonderful answer! Thank you so much, Colin!

Happy New Year :sparkles::tada::confetti_ball:!!!


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