Saved R files (rds files), workflows, meta-data files, and manuscripts of interest.

bash07012021.R; just a simple R script that will run dada2 via R/bash. 

caddis-stripped-06262021.RDS; R session containing the final phyloseq object for n=95 samples from April-2021 time sampling. Created using dada2/phyloseq default settings.

caddis_meta.csv; file meta-data (sample names, sample types) for all 95 samples from April-2021 time sampling, also for Catie Williams-REU.

caddis_toy_meta.csv; subset of meta data from 12 samples, used as small dada2 tutorial for Catie Williams-REU.

fly-microbiome-07062021.csv; Insect microbiome studies used for initial comparison study of MT-caddis flys to other insects. Note, not comprehensive, focused mainly on studies where Earth Microbiome primers were used for amplifying V4 16S rRNA gene for direct comparison with our samples. Put together for Catie Williams REU.

insectcompare_07072021.csv; metadata and other information for comparative analyses of insect populations, specifically Caddis Flys from April 2021 sampling and several publically available sample types.

insectcompare_07082021.csv; Subset of 'insectcompare_07072021.csv', amplicon sets selected where read depth was above 5000 reads/sample.

tutorial_dada2_to_phyloseq.md; commands used to process amplicon sequencing through dada2 (v1.16; latest as of May 2021). For the workflow, just used 12 samples
versus all (n=95) as this would take ~12 hours total to run through Desktop mac-osx.
Little to no deviation in commands from the defaults used in the dada2 tutorial (https://benjjneb.github.io/dada2/tutorial.html), just removed error plotting portions, read tracking steps.

most_used_commands.md; an overview of phyloseq. Still working on this.

tutorial_stats.mds; an overview of some stats commands that can be used in phyloseq. Still working on this.

tutorial_unix.md; a brief overview/tutorial of unix (or unix-like) commands for working on an osx terminal. NOTE, line of the grey area can be directly copied and 
pasted into terminal, press enter, see the output. The output of this tutorial is from Tony's computer.

manuscripts.txt; a collection of manuscript web-links of interest.

bash07012021.R; a simple R script for processing amplicons using dada2 in one command with defaults. 

caddis_metaG_rpkg.txt; functional gene frequencies in metagenomes collected from Cherry Creek (April 7 2021). Genes (databases of genes) were downloaded from Bay 2021 Nature Micro from Greening group @ Monash, n=49 total.


```
echo "hello world"
```