make write.paper

project
|- README		# the top level description of content (this file)
|
|- doc/			# documentation for the study
|  |- notebook/		# preliminary analyses (dead branches of analysis)
|  +- paper/		# manuscript(s), whether generated or not
|
|- data			# raw and primary data, are not changed once created
|  |			#  the files in this directory are not maintained in repo
|  |- references/	# reference files to be used in analysis
|  +- raw/		# raw data, specifically fastq files and output from fastq.info
|     |- '\d{6}'	#   YYMMDD stamp for when the libraries were sequenced					
|     |- no_metag	#	mouse data from the run with no metagenomes
|     +- w_metag	#	mouse data from the run with metagenomes
|
|  +- process/		# cleaned data:
|     |- '\d{6}'	#   YYMMDD stamp for when the libraries were sequenced					
|     |- noseq_error	#   OTU assignments when there are no seq errors/chimeras
|     |- no_metag	#	mouse data from the run with no metagenomes
|     +- w_metag	#	mouse data from the run with metagenomes
|
|- code/		# bash and R 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
|
|- scratch/		# temporary files that can be safely deleted or lost
|
|- Kozich_AEM_2013.Rmd 	# executable Rmarkdown for the original Kozich et al
|			# AEM 2013 manuscript
|- Kozich_AEM_2013.md	# Markdown (GitHub) version of the *Rmd file
|- Kozich_AEM_2013.html	# HTML version of *.Rmd file
|
+- Makefile		# executable Makefile for this study