OTU clustering cannot accept paired-end sequences as input

I want to do my analysis based on OTUs (Vesearch Plugin). To do this, I used demux as an input to dereplicate the sequences but it gave the error below.

There was a problem with the command:
(1/1) Invalid value for '--i-sequences': Expected an artifact of at least
type SampleData[Sequences] | SampleData[SequencesWithQuality] |
SampleData[JoinedSequencesWithQuality]. An artifact of type
SampleData[PairedEndSequencesWithQuality] was provided.

I do not know how to solve this error! Admittedly it needs a special file, but there is a question why this command dose not accept the demux file or what file should provide!?

*I checked the path. Everything is OK.


Hello again,

You need to join your paired-end reads before dereplicating. (And you should probably quality filter them as well.)

This is described in this tutorial: https://docs.qiime2.org/2020.11/tutorials/read-joining/


Thanks @colinbrislawn
Is it possible rep-seq provided via DADA2 to dereplicate in Vesearch?
Thank for the quick reply.

Is the rep-seqs output of DADA2 one of these artifact types?

Expected an artifact of at least
type SampleData[Sequences] | SampleData[SequencesWithQuality] |
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Not at all. As I told at first, I used demux file (not rep-seq file provided from DADA2).
Hopefully, I solved the error with your help.
I am asking a relevant question in this regard.
I have merged some groups table and sequences. I need to know is it possible I use them in vesearch to convert them to OTUs? If I want to start from scrach I have to spend more time that is why I am asking if there is a one way/shortcut then I do that to produce OTUs from ASVs! :slightly_smiling_face:
Thanks a lot

I think I am having some trouble understanding your goal.

Are you trying to take your ASVs made with DADA2 and cluster them into OTUs using vsearch?

My previous rep.seq [ASVs] is available. I need to produce OTUS from the ASVs. Is it possible to do that?

Yes it is possible. It is discussed at length in this thread:

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note: I changed the title of this topic

@TurboQiimer in the future please use more descriptive titles. They make it much easier for other users with similar issues to find relevant advice, when searching in the future!

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