How to import demultiplexed paired-end reads?

I guess so. I am totally new to Qiime world. So right now my data is: Each sample I have one forward.fastq and one reverse.fastq file; for whole sample, I have one forward index.fastq and one reverse index.fastq. In this case, could you please let me know how to turn these files to artifacts? Thank you very much!

Hi @savan,

I can’t remember if the functionality you would need to import that type is available in qiime2 yet or not. Someone can comment if it is…

However, I had a similar dataset a while back which I was only able to import into qiime2 by first going through qiime1’s, as explained in more detail in this thread.
Hope that helps!

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Hello Sevan,

If all the samples are already in separate files, you don’t even need the barcodes. You can just import all your samples using the fastq-manifest-format

If you get stuck, you can post the full command you ran and any output it made, and we can help you get started.

Good luck!


Oops. It looks like I read the original question wrong, for some reason I thought there were a total of 4 multiplexed files (F-sequences, R-sequences, F-indexes, and R-indexes). @colinbrislawn’s directions are absolutely correct, thanks for the catch Colin! My apologies if I sent you on a wild goose chase!


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