/Final_PAFL_Trophicstate

This is the repository for the manuscript "Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla" written by Marian L. Schmidt, Jeffrey D. White, and Vincent J. Denef.

Primary LanguageHTMLMIT LicenseMIT

Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla.

Authors: Marian L. Schmidt, Jeffrey D. White, and Vincent J. Denef

Accepted by Environmental Microbiology on November 19th, 2015

- Link to the article: http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.13143/abstract

- Link to the rendered code file for production of all figures and statistical analyses: http://rpubs.com/marschmi/133626 (Created with the SoMiLakes_PAFL_Analysis.Rmd file)

This is the repository for the manuscript "Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla" written by Marian L. Schmidt, Jeffrey D. White, and Vincent J. Denef. The raw data can be obtained from the Sequence Read Archive at NCBI under accession SRP066777, which are associated with BioProject PRJNA304344.

####Information about this repository:

Original fastq files:

The original Fastq files were submitted to the NCBI sequence read archive under BioProject PRJNA304344, SRA accession number SRP066777.

Code Files:
  1. SoMiLakes_PAFL_Analysis.Rmd includes all of the data analysis!
    • SoMiLakes_PAFL_Analysis.html is the rendered html of the above file.
  2. Functions_PAFL.R has all of the functions written or sourced for the data analysis in the SoMiLakes_PAFL_Analysis.Rmd code file.
Directories/Directory Set up:
  1. Nov6_FWDB_Silva: Includes the raw output files from the mothur pipline and the raw environmental data collected for the project. Including:
    • Mothur cons.taxonomy file: SoMiLakes_copy_FWDB.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.0.03.cons.taxonomy
    • Mothur shared file: SoMiLakes_copy_FWDB.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.shared
    • mothur batch file: Nov4_FWDB_batch
  2. Nov6_FWDB_Silva/Nov_alpha_data: Includes the 100X sub-sampled (rarefied) data for within-sample (alpha) diversity calculations. Also includes otu_melt, which is a large file containing the otu abundance counts for each sample in long-format.
    • 100X Sub-sampled Inverse Simpson: InvSimpson100_summed
    • 100X Sub-sampled Observed Richness: ObservedRichness100_summed
    • Each OTU abundance per sample: otu_melt
  3. FWDB_Figures: A home for all the figures created in the SoMiLakes_PAFL_Analysis.Rmd file.
    • This is where all the figures will be outputted.

Note: This project is under the general MIT License.