QIIME2 with DADA2, demultiplex paired ends sequences

I am a new user of QIIME2. I want to use DADA2 on qiime2 to analysis my 16S Miseq data in V4 region, with 150bp for each single ended reads.
My data includes, R1_1st.fastq, R2_1st.fastq, I_1st.fastq, mappingfile_1st for 101 samples. Also R1_2nd.fastq, R2_2nd.fastq, I_2nd.fastq, mappingfile_2nd for 94 samples. Not demultiplexed data. And the barcode in the 1st batch is the same as the second batch. So my question is, How to deal with this kind of data? I saw some suggestions on not merged the data before using DADA2. I also know that DADA2 do not support for not demultiplexed data. Could any one give me some suggestions?
Thanks in advance.

Hi @Lu_Yang,
Thanks for posting!

That is correct. You will want to import, demultiplex, and dada2 your runs separately prior to merging, as I detail below.

For each sequencing run, you will need to:

  1. import to QIIME 2
  2. Demultiplex with this command
  3. Denoise with dada2

And finally merge your feature tables and sequence files.

These steps are covered in this tutorial and I would suggest getting familiar with that workflow using those tutorial files prior to attempting to use your own data — the process will be much faster and make you more confident with the process.

I hope that helps!

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Thanks so much! it works well! I used to play with QIIME1. This time came to QIIME2. At first, found myself lost. Now i know the flow clearly. Thanks so much!

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