Merged sequence 100%OTU picking

Hi,

I have the demultiplexed 16S sequence having merged, is that possible to deal with in QIIME2? Which version of import shall I use?
Thanks in advance.

Hi @Lu_Yang!

Do you mean you have paired-end sequences that you have joined outside of QIIME 2? If so, you will need to wait for QIIME 2 2017.11, which should be released later today (if everything goes according to plan!).

If this isn’t the case, can you please provide some more details so that I understand your question? Thanks! :t_rex:

Good morning,

If you have already merged the forward and reverse reads, so that you have one fastq files for each sample, you could try using the Fastq manifest format for importing. See this tutorial.
https://docs.qiime2.org/2017.10/tutorials/importing/#fastq-manifest-formats

Let us know how that works,
Colin

Hi, @thermokarst,

Correct! What I mean is exactly the same as what you got! WOW! Congrats to our users! New version QIIME is coming! Looking forward!

Best.

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Hi, @colinbrislawn,

Thanks for your reply. Good news to me.
Does that mean that I can regard my merged paired ended sequences import as SingleEndFastqManifestPhred33(my Phre is 33) format? All the later analysis can be regarded as single ended reads processing in DADA2 also?

Thanks so much.

Hi @Lu_Yang! Unfortunately @colinbrislawn’s suggestion is incorrect w.r.t. DADA2 — it would be a bad idea to run merged sequences through DADA2 as single-end reads (it sounds like that is your plan), because DADA2 operates on the forward and reverse reads separately, then merges the reads as part of the denoising process. You could take @colinbrislawn’s advice if you wanted to run your reads through q2-deblur instead of q2-dada2 (as single-end reads). At this point though, it might be best to wait for 2017.11 to come out, which has official support for joined reads. Thanks!

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Hi, @thermokarst,

Thanks so much for your advice. I will wait for the new version’s come out.

Best

Good catch Matt. DADA2 has it’s own pipeline and assumptions that are a little different.

The plugins q2-deblur or q2-vsearch will work with you paired end reads right now.

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

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