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

dataset
posted on 06.05.2022, 15:59 by Jarrod ScottJarrod Scott
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).

ITS (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


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