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

<b>Output files from the No 2. Data Preparation Workflow</b> page of the SWELTR high-temp study.<br>Workflow objects:<br><b>data_prep_ssu18_wf.rdata: </b>contains all variables and phyloseq objects from the 16s rRNA part of data prep pipeline. To see the <b>Objects</b>, in R run <i>load("data_prep_ssu18_wf.rdata", verbose=TRUE)<br></i><br><i><b>data_prep_its18_wf.rdata: </b>contains all variables and phyloseq objects from the ITS part of data prep pipeline. To see the <b>Objects</b>, in R run <i>load("data_prep_its18_wf.rdata", verbose=TRUE)</i></i><i><i><br></i></i>Additional files:<br>For convenience, we also include raw phyloseq objects(before removing contaminants, etc.), as well as individual ASV, taxonomy, sample data tables. <br><br>Each zip file contains the following:<br><b>*_ps.rds</b>: raw phyloseq object.<br><b>*_full_seq_table.txt</b>: Tab-delimited text file of ASV table.<br><b>*_full_tax_table.txt</b>: Tab-delimited text file of taxonomy table.<br><b>*_sam_tab.txt</b>: Tab-delimited text file of sample table.<br><b>*_full.fasta</b>: Fasta formatted file of all ASV sequences<b>*_ps_work_o.rds</b>: Phyloseq object <i>after</i> removing contaminants. <br><br><b>data_prep_wf_ssu.zip</b>: data packet for 16S rRNA data.<b>data_prep_wf_its.zip</b>: data packet for ITS data.<br>Source code for the workflow can be found here:https://github.com/sweltr/high-temp/blob/main/data-prep.Rmd <br><i><i></i></i><br><br>