Merge paired reads with dada2

[Stream_biofilm (Danny W)]

Hello,
I am working with an illumina Miseq paired end amplicon dataset using dada2. I recently completed a similar project using Qiime1 and felt confident in what I was doing. I’m a little confused with when to merge the paired end reads in the dada2 pipeline. Is this a step I should do before dada2 (using PEAR etc.) or do I do it after dada2? I see there are two dada2 options for paired and single reads and I’m not sure if this is referring to paired end sequencing or referring to the sequences already being paired.

Thanks for the help,
Danny

[jairideout (Jai Ram Rideout)]

Hi @Stream_biofilm! You'll want to import your unjoined paired-end sequences and use q2-dada2 to denoise them. dada2 will join the reads for you during denoising. It's recommended that you avoid joining your reads prior to running DADA2. See these forum topics for more details:

Join paired ends of already demultiplexed sequences

I could not found any tutorial that shows how to join paired ends of demultiplexed data. I tried to join each sample individually using “Atacama soil microbiome” tutorial, but it did not worked, cause it needs a barcode file. How can I do it?

Import demultiplexed joined reads (R1+R2 joined)

Dear colleagues, I am a new Qiime 2 user and I am attempting to import joined fastq files (this means that I have only one fastq per sample that includes R1+R2 joined). I am not sure how to import it into Qiime 2 in order to do quality filtering with DADA2. Thank you!

[Stream_biofilm (Danny W)]

@jairideout Thanks for the quick and informative response!

[jairideout (Jai Ram Rideout)]

The QIIME 2 2017.11 release has expanded support for analyzing paired end reads! See the paired end reads community tutorial for more details.