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biocore / q2-greengenes2

A QIIME 2 plugin for interaction with the Greengenes2 database
BSD 3-Clause "New" or "Revised" License
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Difference in number of ASV when using 2022.10.backbone.full-length.nb.qza and using 2022.10.backbone.full-length.fna.qza ? #21

Open hites77 opened 1 year ago

hites77 commented 1 year ago

I found more number of ASV when using 2022.10.backbone.full-length.nb.qza file directly in QIIME2 for V3-V4 sequence taxonomy prediction in comparison to using 2022.10.backbone.full-length.fna.qza via greengenes2 plugin. So want to know which way is better than other ?

wasade commented 1 year ago

Hi @hites77,

I apologize for the delay in seeing this. At the moment, I'm primarily monitoring the QIIME 2 forum for questions.

I'm not sure I understand the question. The .nb file is used for taxonomy classification, whereas the .fna file is just the sequences themselves. Could you provide the commands used?

Best, Daniel

hites77 commented 1 year ago

Here are the commands:

  1. Qiime2 commands using full length nb file qiime feature-classifier classify-sklearn --i-classifier amplicon/data/taxonomy/2022.10.backbone.v4.nb.qza --i-reads rep-seqs-dada2.qza --o-classification taxonomy.qza

  2. Qiime2 command using greengenes2 plugin qiime greengenes2 non-v4-16s --i-table table-dada2.qza --i-sequences rep-seqs-dada2.qza --i-backbone 2022.10.backbone.full-length.fna.qza --o-mapped-table table_filtered.gg2.biom.qza --o-representatives rep_seqs_filtered.gg2.fna.qza qiime greengenes2 taxonomy-from-table --i-reference-taxonomy 2022.10.taxonomy.asv.nwk.qza --i-table table_filtered.gg2.biom.qza --o-classification table_filtered_gg2.taxonomy.qza

As I mentioned, previously, this two methods are giving different number of ASVs, so which one of them will be more technically correct ?