Extracting sequencing data from qiita

The metadata on qiita do not have barcode sequence column. At least not the ones I checked. Then how do we demultiplex outside qiita?

Hi @Negin,

Not an answer, but I moved this to it’s own topic.

Best,
Justine

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Hi @Negin,
You should be able to download the demultiplexed files right from Qiita as this demultiplexing is a required step before data can be made public.
When you are viewing the “processing graph”, simply click on the triangle that has (demultiplexed) under it and you should have access to the demux files to download.

Right. I know that but I am not sure what type of data that is and how to import it into qiime2. The suffix is .demux so not sure what format it is.

Hi @Negin,
Hmm, perhaps @antgonza can comment regarding the format of what seqs.demux files are and how they can be imported into QIIME2. They look like some sort of zipped file to me but I’m not sure exactly either.

But to go back to your original inquiry:

The “barcode” column should be in the prep info file that you download, do the studies you are looking at not contain this in the prep file? I wonder if perhaps those are some of the older exceptions before this was a requirement…

Without barcode info you couldn’t…I’d also comment that, depending on the goal here, perhaps you don’t need to do this outside of Qiita at all. If you are trying to do a metanalysis of various studies from Qiita (but you want to do the actual analysis outside of Qiita), another option is to just download the processed biom files and merge them to use downstream. That way you don’t need to burden yourself with all the processing steps and you can go right to analysis.

Hi Mehrbod,

From prep info, do you mean the metadata that can be downloaded under Sample information tab?

I am fine with doing everything inside qiita. The only thing is I need to combine this with my own data and I had trouble uploading mine to qiita. Hence, thought of downloading from qiita.

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Hi @Negin,
No, not under the sample information tab. See the image in my last post with the “Prep info” button underlined in red. In Qiita, the sample information file is where you have information about your sample’s biology, while the “Prep info” hold information about how the sequencing files were generated which also includes information about primers, the barcodes etc.

If you’re having trouble with uploading your data into Qiita you can also email the support team [email protected] and that might recruit help for you quicker. That way more members of the Qiita team will read those than here.
Hope that helps!

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Thanks for the clarification. I read about these two file types and now I understand better.

Yep. I contacted them and now things are clearer. Apparently, there has been a unique issue with my study ID in that some admins had changed permissions for my study ID by mistake. lol. They fixed it now :slight_smile:

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