(high-temp) No 3. Filtering: (16S rRNA/ITS) Output

Output files from the No 3. Filtering Workflow page of the SWELTR high-temp study. ASV filtering for 16S rRNA & ITS using a) Arbitrary filtering, b) PERFect (PERmutation Filtering test for microbiome data), and c) PIME (Prevalence Interval for Microbiome Evaluation) Workflow objects:
filtering_wf.rdata: contains all variables and phyloseq objects from 16s rRNA and ITS ASV filtering. To see the Objects, in R run load("filtering_wf.rdata", verbose=TRUE)
Additional files:
For
convenience, we also include
individual phyloseq objects for each filtered data set.
Arbitrary:
ssu18_ps_filt.rds: phyloseq object for Arbitrary filtered 16S rRNA ASVs.
its18_ps_filt.rds: phyloseq object for Arbitrary filtered ITS ASVs.

PERfect:
ssu18_ps_perfect.rds: phyloseq object for PERfect filtered 16S rRNA ASVs.
its18_ps_perfect.rds: phyloseq object for PERfect filtered ITS ASVs.

PIME:
ssu18_ps_pime.rds: phyloseq object for PIME filtered 16S rRNA ASVs.
its18_ps_pime.rds: phyloseq object for PIME filtered ITS ASVs.
Source code for the workflow can be found here:https://github.com/sweltr/high-temp/blob/master/filtering.Rmd