Hi Nicholas. Could you please explain ahow to filtering a taxonomy, so you can remove IDs not in the sequences and re-create human-stool weights?
If you run
qiime rescript filter-taxa --help, you'll see that you can simply provide the sequence file to the
--m-ids-to-keep-file parameter. Then you provide your taxonomy file with the
--i-taxonomy parameter. This will remove any taxonomy with IDs that are not found within the sequence file.
Thank you Mike. I tired the next code
qiime rescript filter-taxa --m-ids-to-keep-file silva-138.1-ssu-nr99-seqs-V3V4-uniq.qza --i-taxonomy readytowear-master/data/silva_138_1/full_length/human-stool.qza --o-filtered-taxonomy human-stool-V3V4.qza
but "human-stool.qza" is not a FeatureData[Taxonomy] file, is an FeatureTable[RelativeFrequency].
I am trying to create a silva-138.1-ssu-nr99-V3V4-stool-classifier.qza
I could create silva-138.1-ssu-nr99-V3V4-classifier.qza but I don't have human-stool-V3V4.qza so error "Number of priors must match number of classes" appears.
I could create silva-138.1-ssu-nr99-stool-classifier.qza because I have humann-stool.qza with full 16S from redytowear. I couldn't find the V3V4 version.
I am analyzing 16S V3V4 Illumina sequences so I think I need the V3V4 trained classifier.
Hi @imonteroo ,
If you are trying to create new weights with a different taxonomy you will need to follow this tutorial from the beginning:
The readytowear weights are built using specific taxonomies (as described in the readytowear repository) so will only work with those taxonomies.
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.