(high-temp) No 2. Data Preparation (16S rRNA/ITS) Output

**Output files from the No 2. Data Preparation Workflow** page of the SWELTR
high-temp study.

Workflow objects:

**data_prep_ssu18_wf.rdata:** contains all variables and phyloseq objects from
the 16s rRNA part of data prep pipeline. To see the **Objects** , in R run
_load("data_prep_ssu18_wf.rdata", verbose=TRUE)
_

_**data_prep_its18_wf.rdata:** contains all variables and phyloseq objects
from the ITS part of data prep pipeline. To see the **Objects** , in R run
_load("data_prep_its18_wf.rdata", verbose=TRUE)__

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Additional files:

For convenience, we also include raw phyloseq objects(before removing
contaminants, etc.), as well as individual ASV, taxonomy, sample data tables.

Each zip file contains the following:

***_ps.rds** : raw phyloseq object.
***_full_seq_table.txt** : Tab-delimited text file of ASV table.
***_full_tax_table.txt** : Tab-delimited text file of taxonomy table.
***_sam_tab.txt** : Tab-delimited text file of sample table.
***_full.fasta** : Fasta formatted file of all ASV sequences

***_ps_work_o.rds** : Phyloseq object _after_ removing contaminants.

**data_prep_wf_ssu.zip** : data packet for 16S rRNA data.

**data_prep_wf_its.zip** : data packet for ITS data.

Source code for the workflow can be found here:

https://github.com/sweltr/high-temp/blob/main/data-prep.Rmd

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