(high-temp) No 4. Taxonomic: (16S rRNA/ITS) Output

**Output files from the No 4. Taxonomic Workflow** page of the SWELTR high- temp study. In this workflow we used the microeco package for taxonomic assessment. We first converted each phyloseq object into a microtable object using the file2meco package. **taxa_wf.rdata** : contains all variables and phyloseq objects from 16s rRNA and ITS ASV taxonomic assessment. To see the Objects, in R run _load("taxa_wf.rdata", verbose=TRUE)_ Additional files: For convenience, we also include individual phyloseq and microtable objects (collected in zip files). _I_** _TS (its_taxa_objects.zip)_ :** **its18_ps_work_me.rds** : microtable object for the FULL (unfiltered) ITS data. **its18_ps_filt_me.rds** : microtable object for the Arbitrary filtered ITS data. **its18_ps_perfect_me.rds** : microtable object for the PERfect ITS data. **its18_ps_pime_me.rds** : microtable object for the PIME ITS data. _**16S rRNA (ssu_taxa_objects.zip):**_ **ssu18_ps_work_me.rds** : microtable object for the FULL (unfiltered) 16S rRNA data. **ssu18_ps_filt_me.rds** : microtable object for the Arbitrary filtered 16S rRNA data. **ssu18_ps_perfect_me.rds** : microtable object for the PERfect 16S rRNA data. **ssu18_ps_pime_me.rds** : microtable object for the PIME 16S rRNA data. For one of the 16S rRNA analyses we looked at family-level diversity of major bacterial phyla. For this analysis, we renamed NA ranks by the next highest named rank. For example, ASV13884 was unclassifed at family level, so the _NA_ was replaced with the next highest named rank (in this case order). Therefore the family-level classification for this ASV was changed to _o_Polyangiales_. Doing this allowed us to include uncalssifed abundance in our analyses. We include the following phyloseq objects containing the modifed taxonomies. **ssu18_ps_work_clean.rds** : modified phyloseq object for the FULL (unfiltered) 16S rRNA data. **ssu18_ps_filt_clean.rds** : modified phyloseq object for the Arbitrary filtered 16S rRNA data. **ssu18_ps_perfect_clean.rds** : modified phyloseq object for the PERfect filtered 16S rRNA data. **ssu18_ps_pime_clean.rds** : modified phyloseq object for the PIME filtered 16S rRNA data. Source code for the workflow can be found here: https://github.com/sweltr/high-temp/blob/master/taxa.Rmd