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.
By the way, I expected to have higher match query in comparison to ASVs output, but it was surprisingly too low!!!
I realized that I have skipped the main step, clustering.
I picked up De-Novo. Sadly it gave a wired error!
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.
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
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!
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.