Hello,
I am trying to cluster my sequences into OTUs. For demultiplexing I used an another pipeline (i.e., Stacks) due to the nature of my data. Then I quality fitered and trimmed primer sequences and Illumina dapters with Trimmomatic. So now I uploaded the data into Qiime and I would like to produce a feature table of my data. I read in some Qiime 2 tutorial that the data need to be:
-
Pair end reads are merged
-
Non-biological sequences are removed
-
Reads are trimmend to the same length
-
Low quality reads are discarded
With Trimmomatic I performed all the steps except for the truncation of the reads to the same length. I set a limit of 100 bp for the sequences to be kept. So now my reads are of minimmum legth 100 bp, the primer and adapter sequences are removed, they were quality filtered based on Q-score, but they are of varying lengths.
My sequences look like this:
This quality plot correspond to the merged, quality filtered and without primer and adapter sequences reads. This is the summary of lengths:
Is there a way to cut the sequences to the same length in Qimme2 without doing anything else? I would like to cut all the sequences to a length of 300 since I am working with ITS-2. I am aware of DADA2 and Deblur being able to do this before denoinsing. I know that before OTU clustering I need to dereplicate my sequences with:
qiime vsearch dereplicate-sequences
--i-sequences joined-ITS-2.qza
--o-dereplicated-table table-dereplicated-ITS-2.qza
--o-dereplicated-sequences rep-seqs-ITS-2.qza
and then I can performed the clustering with:
qiime vsearch cluster-features-de-novo
--i-table table-dereplicated-ITS-2.qza
--i-sequences rep-seqs-ITS-2.qza
--p-perc-identity 0.99
--p-threads 12
--o-clustered-table table-dn-99-ITS-2.qza
--o-clustered-sequences rep-seqs-dn-99-ITS-2.qza
Thank you very much for your help!! 
