Scripts for reproducing analyses from Hogle et al. L&O Letters.
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metadata
scripts
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README.md

README.md

Introduction

Scripts for reproducing analyses from Hogle et al. L&O Letters. This project investigated the production of different classes of iron-binding ligands, iron concentrations, macronutrient concentrations, and phytoplankton and bacterioplankton assemblage composition in iron amended microcosm incubations conducted in oligotrophic waters collected off the Southern California Bight.

Data and Code

Scripts for reproducing the bacterial OTU analyses are found in the scripts folder and metadata is located in the metadata folder. These files are also hosted at a Figshare repository

Required Software

NCBI SRA Toolkit v2.7.0

USEARCH v8.1.1861

RDP classifier v2.12

R v3.3.0

R Libraries

  • phyloseq
  • ggplot2
  • reshape2
  • grid
  • vegan
  • DESeq2

How to reproduce analysis...

After installing the above software and adding it to your path run the scripts in the following order

bash sequence_processing.sh
R preprocessing.R
R richness.R
R bar_plots.R
R diff_abundance.R
R ordination.R

All scripts are heavily documented so open them in a text editor (or R studio) to see what is really going on. I would recommend using Rstudio so that you can perform each step interactively.

The sequence_processing.sh script should create a directory hierarchy for the project that is self explanatory. It will also connect remotely to the NCBI SRA to download the sequecing data. For the sake of completeness, you can find the links to the NCBI SRA below: