How to remove Chimeras from the Feature Table using Vsearch Plugin?

Technical Support
1

Hi There,

I was successful to generate OTUs (rep-seq and table) with Vesearch Plugin. Then I generated my classification file with the Vesearch classifier. When I wanted to visualize the file I got the following error!

I passed these steps: demux file > join-pairs > dereplicate-sequences >
uchime-denovo > I used non.chimeras sequence and generated table from Vesearch > I used the two with metadata in Vesearch classifier > Finally I used this method "qiime taxa barplot" to visualize the taxa.

Screenshot from 2021-01-22 19-44-45

By the way, I expected to have higher match query in comparison to ASVs output, but it was surprisingly too low!!!

Screenshot from 2021-01-22 19-53-46

I am using Qiime2 Version 2020.08.

Thanks
Qiimer

2

I realized that I have skipped the main step, clustering.
I picked up De-Novo. Sadly it gave a wired error!
Screenshot from 2021-01-22 21-26-34

The modified steps:
demux file > join-pairs mehod > dereplicate-sequences method >
uchime-denovo method > I used non.chimeras sequence and table generated from Vesearch plugin > I applied the de-novo clustring features > faceed to the error above.

How to solve this error? Did something go wrong?

3

I checked out these threads but could not grab something.

6

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!

your previous title (“classification visualization error”) does not clearly describe the error you are seeing.

7

Thanks dear @Nicholas_Bokulich
At the moment I have a clustering problem: Feature IDs do not match with Sequences as I read in the last error.
I changed the topic from “barplot error message: feature IDs found in the table are missing from the taxonomy” to “Vsearch clustring error message: feature IDs found in the table are missing from the sequences”.
@cherman2

9

I think I used the non-chimera sep-seq FeatureData[Sequence] while the chimeras are still present in the table FeatureTable[Frequency]!!! I have no any idea how to remove the chimeras IDs from the table. The error is for that!

This command has no output for the table:

qiime vsearch uchime-denovo
–i-sequences OTUs-clustered-Rep.Seq.qza
–i-table OTUs-clustered-Table.qza
*–o-chimeras vesearch-chimeras.qza *
*–o-nonchimeras vesearch-non.chimera-sequences.qza *
–o-stats vesearch.sequence-status.qza

I changed the topic from " Vsearch clustring error message: “feature IDs found in the table are missing from the sequences” to “How to remove Chimeras from the Feature Table in Vsearch Plugin”

Thanks
Qiimer

11

Hello @TurboQiimer,
I am going to preface this with the fact that I am not super familiar with vsearch. However, I think I have an answer for you. Let me know though If this doesn’t help and we will try to debug more.

So I think the solution to your issue is found in this chimera tutorial:
https://docs.qiime2.org/2020.11/tutorials/chimera/
It has a section on filtering input tables that I think is pertinent. https://docs.qiime2.org/2020.11/tutorials/chimera/#filter-input-tables-and-sequences
I think this should filter the chimeras out of your table so that you can run cluster-features-de-novo without those errors.
I hope this helps!
Chloe :turtle:

3 Likes
13

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.