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

dataset

posted on 06.05.2022, 13:12 by Jarrod ScottJarrod Scott

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)

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