I want to cluster my short reads(really short ~18nts) by using vsearch open-reference. However,I need to convert my fastq file --> SampleData–>featureData. It is fine for the first conversion. When I use vsearch to get featureData from SampleData, I got the error that all of reads are removed. The command is this:
qiime vsearch dereplicate-sequences
After checking the posts here and source codes of vsearch as well, I found that the reason of all of my reads were filtered out is due to the parameter set in vsearch ‘–minseqlength’ which is set to 32 as default. Unfortunately, I couldn’t find a way in qiime2 to twist this parameter (maybe I miss this). Anyone has suggestion to avoid this?
Also, if I try to use vsearch to dereplication, how could I convert the outputs there to .qza that I can move forward to the clustering in qiime2?