joined reads before deblur

[Mehrbod_Estaki]

Hi @Lu_Zhang,

@Lu_Zhang

I found your current protocol paper about qiime2 2019.10 version

Thanks for the reminder that I should update that to reflect the newest version of QIIME 2. Btw, you if you are using the newest 2020.6 release, to follow that protocol, you will have to change one thing, as per the notice here when you get to the core-metrics step you'll need to change the n_jobs parameter parameter to n_jobs_or_threads which was recently changed.

As per your other questions:

@Lu_Zhang

I guess if my joined-reads is without quality score, I couldn’t use it as input for deblur?

You couldn't use the q2-deblur plugin, but I believe the stand-alone deblur does allow fasta files.

@Lu_Zhang

So I should join my raw pair-end reads first.

If your plan is to use Deblur, then yes! If you use DADA2, you should not join prior as DADA2 will do merging on its own.

@Lu_Zhang

But there is no primer removal procedure here.

Yes and no. Technically, neither DADA2 or Deblur have specialized primer/adapter removal procedures, the way something like q2-cutadapt does, though both offer options to do a fixed trim from either direction which can be used to trim primers. Deblur does offer options to trim from both the 5' and 3'. --p-trim-length will cut from the 5', and --p-left-trim-len will trim from the 3'. However, I personally would recommend using q2-cuatadapt to remove primers prior to merging/filtering, and making sure to enable the --p-discard-untrimmed tag, which will also discard any reads that don't have the primers in them. I find this does a great job of filtering junk reads.

Hope this helps!