How do I convert my rep-seqs.qzv file to a biom file to visualise the OTU-sample relationship?

Hi @thermokarst ,

How do I convert my rep-seqs.qzv file to a biom file to visualise the OTU-sample relationship?

Also, where do I find the fasta and taxonomy file for Silva? I’ve changed to using the Silva 138 99% OTUs full-length sequences database now.
Would it be from this link? Under Silva_132_release.zip? Because l know I will have to convert the database files into artifact files to be accepted as an input file into QIIME. And does it matter if its 138 trained on 132?

(https://www.arb-silva.de/download/archive/fileadmin/silva_databases/qiime/Silva_132_release.zip)Archive

I’m assuming this will be the commands I’ll be inputting (this example is using the greengenes database):
qiime tools import
–type ‘FeatureData[Sequence]’
–input-path rep_set/99_otus.fasta
–output-path GG_99_seq_db.qza

qiime tools import
–type ‘FeatureData[Taxonomy]’
–input-format HeaderlessTSVTaxonomyFormat
–input-path 99_otu_taxonomy.txt
–output-path GG_99_taxonomy_db.qza

Hello @Jan,
Is it really important that you use rep-seqs file to create biom file? I have only seen this done using the feature table. This exporting tutorial can help you with export your feature table to a .biom file if that will work for you.

I believe that Silva 132 is archived because there is a new release 138. I think that you can use 132 data (but I am not sure) but if you aren’t curating your own training set you might want to use one of our pre-training classifiers. You can look at our classifiers here :qiime2:

Your commands look good and I would point you to our training feature classifier tutorial if you want to train your own classifier. I find that it is really helpful for understanding what commands are necessary.
Hope this helps!
Chloe :turtle:

Hi @cherman2,

Yeah for exporting the feature table. Thanks for that!

I have been following this link for Silva 138 Classifier SILVA 138 Classifiers

After installing RESCRIPt, I input this command:
qiime tools import
–type ‘FeatureData[SILVATaxonomy]’
–input-path tax_slv_ssu_138.txt
–output-path taxranks-silva-138-ssu-nr99.qza

but received this error message

Screen Shot 2021-06-08 at 2.10.08 pm

I’m not sure what went wrong.

Hello Jan,
I have been looking for this error. I have only been able to find this. This issue was after installing QIIME2 but it might have the same solution. They were able to fix this issue by upgrading to the most recent version of QIIME2.

Let me know if this fixes the issue! Otherwise, come back and we will figure out this issue.
Chloe :turtle:

Hi @cherman2,

Thanks so much for the help. I updated to the latest version of QIIME2 and it works fine now. Cheers.

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