use qiime1 to generate barcode.fastq.gz before using qiime2 to analyze 16s RNA

[terren (h.w)]

Because the data include only paired-end sequences and sample information, I used qiime1(extract_barcodes.py) to generate barcode file.Then, could I use qiime2(version:2019.10.0) to demux?

[RocktimRamenDas]

As far as I am aware. Both are different platforms. I suggest you complete all the process in Qiime 2 itself.

Cheers
Rocktim

[Nicholas_Bokulich]

@terren

Because the data include only paired-end sequences and sample information, I used qiime1(extract_barcodes.py) to generate barcode file.Then, could I use qiime2(version:2019.10.0) to demux?

That is totally fine. I believe after using extract_barcodes.py your data could be imported and demultiplexed using the EMP format protocols as described, e.g., in the moving pictures tutorial.

But where are the barcodes in the original sequences? If they are at the 5' ends of the reads, you can follow this tutorial to import and process the data:

Demultiplexing and Trimming Adapters from Reads with q2-cutadapt

NOTE This tutorial is a work in progress, and is incomplete at the moment. It demonstrates at a high level some of the methods available in the q2-cutadapt plugin available in QIIME 2 2018.2. Please stay tuned here for additional updates as this tutorial is expanded upon in the coming weeks. Multiplexed reads with the barcodes in the sequence reads can be demultiplexed in QIIME 2 using the q2-cutadapt plugin,…

@RocktimRamenDas

As far as I am aware. Both are different platforms. I suggest you complete all the process in Qiime 2 itself.

In general, if something can be done in QIIME 2 it would be best to keep the entire pipeline in QIIME 2 for the smoothest experience. But QIIME 2 is designed to support imports of data in various formats to support flexible pipelines... and QIIME 2 cannot do everything (e.g., support older formats where barcodes are in the header line, and for which extract_barcodes.py is still a valid way to reformat the data prior to importing to QIIME 2).

Good luck!

[terren (h.w)]

Thanks. After extract barcodes from the sequence using extract_barcodes.py, the importing to QIIME2 has been done. Thanks again.