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

<b>Output files from the No 4. Taxonomic Workflow</b> 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.<br><br><b>taxa_wf.rdata</b>: contains all variables and phyloseq objects from 16s rRNA and ITS ASV taxonomic assessment. To see the Objects, in R run <i>load("taxa_wf.rdata", verbose=TRUE)</i><br><br>Additional files:<br><br>For convenience, we also include individual phyloseq and microtable objects (collected in zip files).<br><br>I<b>TS (its_taxa_objects.zip):</b><br><b>its18_ps_work_me.rds</b>: microtable object for the FULL (unfiltered) ITS data.<br><b>its18_ps_filt_me.rds</b>: microtable object for the Arbitrary filtered ITS data.<br><b>its18_ps_perfect_me.rds</b>: microtable object for the PERfect ITS data.<br><b>its18_ps_pime_me.rds</b>: microtable object for the PIME ITS data.<br><br><b>16S rRNA (ssu_taxa_objects.zip):</b><br><b>ssu18_ps_work_me.rds</b>: microtable object for the FULL (unfiltered) 16S rRNA data.<br><b>ssu18_ps_filt_me.rds</b>: microtable object for the Arbitrary filtered 16S rRNA data.<br><b>ssu18_ps_perfect_me.rds</b>: microtable object for the PERfect 16S rRNA data.<br><b>ssu18_ps_pime_me.rds</b>: microtable object for the PIME 16S rRNA data.<br><br>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 <i>NA</i> was replaced with the next highest named rank (in this case order). Therefore the family-level classification for this ASV was changed to <i>o_Polyangiales</i>. Doing this allowed us to include uncalssifed abundance in our analyses. We include the following phyloseq objects containing the modifed taxonomies. <br><br><b>ssu18_ps_work_clean.rds</b>: modified phyloseq object for the FULL (unfiltered) 16S rRNA data.<br><b>ssu18_ps_filt_clean.rds</b>: modified phyloseq object for the Arbitrary filtered 16S rRNA data.<br><b>ssu18_ps_perfect_clean.rds</b>: modified phyloseq object for the PERfect filtered 16S rRNA data.<br><b>ssu18_ps_pime_clean.rds</b>: modified phyloseq object for the PIME filtered 16S rRNA data.<br><br><br>Source code for the workflow can be found here:<br>https://github.com/sweltr/high-temp/blob/master/taxa.Rmd<br><br><br>