lucas-bishop/gregory_sze_reanalysis

reanalysis of 2018 work done by Mia Gregory and Marc Sze

Download the latest release to the directory and decompress

Reanalysis of 2018 work done by Marc Sze Mia Gregory

investigation of the effects of different dna polymerases and storage conditions on sequencing results

Overview

project
|- README          # the top level description of content (this doc)
|- CONTRIBUTING    # instructions for how to contribute to your project
|- LICENSE         # the license for this project
|
|- submission/
| |- study.Rmd    # executable Rmarkdown for this study, if applicable
| |- study.md     # Markdown (GitHub) version of the *.Rmd file
| |- study.tex    # TeX version of *.Rmd file
| |- study.pdf    # PDF version of *.Rmd file
| |- header.tex   # LaTeX header file to format pdf version of manuscript
| |- references.bib # BibTeX formatted references
| |- XXXX.csl     # csl file to format references for journal XXX
|
|- data           # raw and primary data, are not changed once created
| |- references/  # reference files to be used in analysis
| |- raw/         # raw data, will not be altered
| |- mothur/      # mothur processed data
| +- process/     # cleaned data, will not be altered once created;
|                 # will be committed to repo
|
|- code/          # any programmatic code
|
|- results        # all output from workflows and analyses
| |- tables/      # text version of tables to be rendered with kable in R
| |- figures/     # graphs, likely designated for manuscript figures
| +- pictures/    # diagrams, images, and other non-graph graphics
|
|- exploratory/   # exploratory data analysis for study
| |- notebook/    # preliminary analyses
| +- scratch/     # temporary files that can be safely deleted or lost
|
+- Makefile       # executable Makefile for this study, if applicable

How to regenerate this repository

Dependencies and locations

• Gnu Make should be located in the user's PATH
• mothur (v1.XX.0) should be located in the user's PATH
• R (v. 3.X.X) should be located in the user's PATH
• R packages:
  • knitr
  • rmarkdown
• etc

Running analysis

git clone https://github.com/SchlossLab/LastName_BriefDescription_Journal_Year.git
make write.paper