does q2-cutadapt support dual indexed reads?

Hi @LuSanto - thanks for following up!

Makes sense!

I did a bit of digging with @ebolyen on this today — turns out cutadapt 2.3 (the version of cutadapt used by q2-cutadapt 2019.7) doesn’t support CDI strategies. Newer versions of cutadapt support CDI strategies - we are hoping to support that in q2-cutadapt in the future. Thanks!

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Just to clarify (for anyone who stumbles on this thread), q2-cutadapt 2019.10 / cutadapt 2.3 do support UDI strategies (where the forward and reverse barcodes are all unique).

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Hi @LuSanto I am trying to solve the exact same problem (Demultiplexing CDI reads) and I would like to know more about your workaround method.

The only way around was to split the metadata into several files, so each of them only includes a unique F barcode. Then I used cutadapt separately with each metadata file. Finally, I reimported all the .fasq files into a single .qza for downstream analysis.

Did you run the demux-paired command on the .qza file for each metatada file with the unique F barcode?
If so how did you end up with several fasq files? I thought the output of demux-paired is also a .qza

Thank you!

Hi @MG_709,
I run demux on the same .qza input several times, each time with a new metadata file (each containing unique F barcodes). Then I unzipped each .qza output (by manually changing the extension to .zip) and retrieved the demultiplexed .fastq files. Finally I imported all the .fastq files into a new .qza, using a manifest.txt.

Hope this helps!


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