I have been using qiime 2-2022.2 to carry out my analysis. I want to know whether it is possible to generate an OTU table containing the OTU number and its abundance but without the taxonomy units assigned using qiime 2.
Moreover, I want to know how I can generate a table_abundance.tsv.
Also, I have used the denoised output file directly to construct the feature table and assign taxonomy. I want to know whether the procedure that I have followed is correct. The commands that I used are as follows.
(I am assume all the questions are related to the commands you show, please let me know if it is correct! )
On generating a feature table without the taxonomy units, the 'table-dada2.qza' artefact should have the info you are looking for and should not have any taxonomys assignemt in it. So, if I undersatand what you mean, if you export fom it using 'qiime export' command you should get a biom file, which in turn you can convert to feature.tsv by using the biom conversion utility (let us know if you need help for this.)
On your commands, they sound overall reasonable. For what I can note, few potential issues could be the following: in th edenoysing poyro step, you use 240 as trun-len parameter, did you check your quality profile to confirm if this lenght suites your sequences? I would expect a bit longer number for 454 data. For the taxonomic classification step, gg is not updated since long time, so it could be a good thing for you to use Silva too to compare the results. You probably want to use also the 'qiime taxa barplot' command to produce the barchart visualiser with th eobtained taxonomic information.