OTU clustering cannot accept paired-end sequences as input

[TurboQiimer]

Hi
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.

Thanks
Qiimer

[colinbrislawn (Colin J Brislawn)]

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/

Colin

[TurboQiimer]

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

[colinbrislawn (Colin J Brislawn)]

@TurboQiimer

Is it possible rep-seq provided via DADA2 to dereplicate in Vesearch?

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

Expected an artifact of at least
type SampleData[Sequences] | SampleData[SequencesWithQuality] |
SampleData[JoinedSequencesWithQuality]

[TurboQiimer]

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!
Thanks a lot
Qiimer

[colinbrislawn (Colin J Brislawn)]

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?

[TurboQiimer]

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

[colinbrislawn (Colin J Brislawn)]

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

To cluster or not to cluster?

Hello - I would like to bring up a topic that has been discussed before (A quick clarification on clustering) and provide an example from my own analysis. I am looking at one particular taxonomic group within environmental samples of bacterial populations. The method of denoising is dada2, so I am assuming that OTU clustering was not necessary since sequencing errors are accounted for during the denoising process. However, this analysis resulted in many OTU's being defined, some of them quite r…

[Nicholas_Bokulich]

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!