el-ee / otu-frontiers

Code for the analysis of sequence and OTU occurance data to derive optimal taxonomic structures for bacterial communities.

otu-frontiers

Code for the analysis of sequence and OTU occurance data to derive optimal taxonomic structures for bacterial communities.

See original if you want to do anything with this.

I am just messing it up right now, as I struggle to figure out what is happening!

Paper describing technique:

• http://journal.frontiersin.org/Journal/10.3389/fmicb.2013.00342/full

THE FILES

FunFrame Pipeline used to get files to the right starting point:

• http://faculty.www.umb.edu/jennifer.bowen/software/FunFrame.zip
• See http://bioinformatics.oxfordjournals.org/content/29/9/1212.long

Data organization

1. First use this file, which reads in this fasta data by traversing directories & produces otu csv

getOTUs.R

Puts together multiple .fasta files from different directories??

• INPUT: Multiple directories each of which contain a fasta formatted file; specify common file name in variable FILE_NAME. THat is, for the example above, you would set FILE_NAME=data.fasta

• OUTPUT: OTU_MAT.csv This file is then used by the other files

2. After that, you can use this one to get abundance data?

getAbundance.R

? Don't really understand which file here

• INPUT: ./clusterDist_0.12/concordance.fasta

• INPUT: OTU_MAT.csv

• OUTPUT: seq_otu_abundance.csv

Then these are things you can do with that csv file about abundance

analyze_otu_networks.R

• INPUT: ./seq_otu_abundance.csv

• OUTPUT:

plotOTUNetworks.R

• INPUT: /seq_otu_abundance.csv

• OUTPUT: a plot

ggplotNetwork.R

• INPUT: ./seq_otu_abundance.csv

• OUTPUT: a plot

Other files

getNetworkAIC.R

Helper file; used by analyze_otu_networks.R and sampleAICNet.R

sampleAICNet.R

Confused.