Qiime2 2018.4 and 2018.11 greengene

greengenes

(Clara) #1

Hi there,

I have a question here, previously when I analysed my sequencing data, in the step where I generated my otu table, I used greengene in the version 2018.4. However, when I re-run my qiime2, the same step has been updated to 2018.11. My otu table has therefore change with REDUCE number of genera. May I know in this instant, should I use the previous version of otu table or the latest one?

Thanks.

Clara


(Matthew Ryan Dillon) #2

Hi there @Clara! Greenegenes hasn’t been updated in many years — I suspect that you might have some subtle differences in the commands run between the two versions. How about you compare provenance for the two tables to see what has changed? If you need help can you run feature-table summarize on the two tables and share here? Thanks!


(Clara) #3

Hi @thermokarst, here is the link that I found “different” when running the command line, that is why I asked about greengene update

wget -O "gg-13-8-99-515-806-nb-classifier.qza" https://data.qiime2.org/2018.4/common/gg-13-8-99-515-806-nb-classifier.qza

wget
-O "gg-13-8-99-515-806-nb-classifier.qza"
https://data.qiime2.org/2018.11/common/gg-13-8-99-515-806-nb-classifier.qza

Is it not because of this?

And because the two ran were using the same table-dada2, so I would think that the otu table generated will be the same?


(Matthew Ryan Dillon) #4

Hey @Clara! Ah yeah, those are links to pre-trained classifiers, not the original greengenes database itself. It looks like some of the default classifier parameters changed in 2018.6 - is it possible that that is what you are seeing? You could confirm by retraining a greengenes-based classifier using the old settings.