Handling paired-end dual indexed Illumina FASTQ files

[Lou]

Dear QIIME2-community,

I am totally new to QIIME and QIIME2. I want to analyse paired-end dual indexed Illumina reads, which means I have 4 FASTQ files (R1 and R2 with microbial sequences, I1 and I2 with barcode sequences).
I (think I) thoroughly checked the documentation and learned that there was a method in QIIME (Preparing raw Illumina data in different formats for use with QIIME — Homepage), but that you cannot easily use this function in QIIME2 and that you are still working on this (Support paired-end demux with two barcode files · Issue #62 · qiime2/q2-demux · GitHub). The recommendation is to process sequences with QIIME and then analyse the result with QIIME2 (Importing multiplexed paired-end data with separated barcode sequence files - #9 by Mehrbod_Estaki), but I am not able to make this work.
I am using QIIME2 2020.2 via VirtualBox.

I would like to know if there will be a solution to this problem soon? Otherwise I would appreciate any help with using old QIIME python scripts in QIIME2 (if possible) or any other workarounds.
Would it be possible to demultiplex with demux EMP-single two times two files and join forward and reverse reads afterwards?

Thanks a lot!

[Mehrbod_Estaki]

Hi Loui,
Welcome aboard!
I wouldn't hold my breath for this functionality to be released in the near future, I don't see it on the radar for at least the next release. So sticking with the Q1 approach linked in the other post is probably your best bet.

@Lou

but I am not able to make this work.

Can you give us a bit more detail regarding what you tried exactly, and where you were unable to get this to work? Did you follow the instructions in the other thread?

[Lou]

Dear @Mehrbod_Estaki,

@Mehrbod_Estaki

I wouldn’t hold my breath for this functionality to be released in the near future.

Thanks a lot for your reply, that's already very good to know.

Well, I am also new to python and the terminal , so I tried to just type the command "extract_barcodes.py", which does not work because QIIME2 doesn't take any python commands if I understood correctly. I also tried to save the "extract_barcodes.py" script manually and call it in the terminal, which produced another error ("ImportError: cannot import name upper").
But apart from the details, is it possible to somehow activate QIIME(1) python commands in QIIME2? Or do I have to set up QIIME(1) in another Virtual machine and run the python scripts there?

Thank you!

[Mehrbod_Estaki]

Hi @Lou,
Aha, gotcha. Ok so you want to think of QIIME 1 and QIIME 2 as two completely different entities that need to bet set up separately. You can't run scripts from one in another. You'll need to install QIIME 1 separately into a new conda environment, activate it and run the commands from that link specifically there, and once you have got the outputs you need, then activate your QIIME 2 environment and migrate your data there.