Hi there, I'm quite a newbie at bioinformatics so please bear with me!
My lab has decided not to use the DADA2 filter/deblur steps in Qiime2 since it seems to throw up most of our sequencing reads from Illumina MiSeq paired-end sequences.
I used Trim Galore for pre-processing, then AMPtk for quality filtering and to merge my ITS1 Illumina Miseq R1 and R2 files, then finally vsearch for OTU clustering at 97%.
Unfortunately, AMPtk isn't updated often so their UNITE database is not up to date. For this reason, I am trying to do taxonomy calling and stats in QIIME. I was able to do the taxonomy calling in q2, but am unable to convert my sequences into a feature table that is a Qiime artifact (.qza) so I cannot make a bar plot, phylogeny, etc.
I've tried a few different methods but none that have worked at all at converting the files into a qiime artifact I can work with.
Here is something I tried but it didn't work (please note I replaced some of my file path prior to copy and pasting here):
qiime feature-table summarize
--i-table /Users/path/Qiime_out/table.qza
--o-visualization /Users/path/Qiime_out/table_summary.qzv
qiime tools export
--input-path /Users/path/Qiime_out/table_summary.qzv
--output-path /Users/path/Qiime_out/exported_table/
(this did not create a .biom file so I could convert to a .qza)
Any help or input is greatly appreciated!