Porites_competition

Using this repository

This repository contains scripts and code. To obtain raw data required to run these scripts you should do the following;

1. Checkout this repository

git clone https://github.com/China2302/Porites_competition.git

2. Download the raw data and unpack it from within the project repository.

cd Porites_competition
wget 'http://data.qld.edu.au/public/Q5999/china2302/Porites_competition/data.tgz' -O data.tgz
tar -zxvf data.tgz

# This is a much larger file required for some analyses only
wget 'http://data.qld.edu.au/public/Q5999/china2302/Porites_competition/data.transcriptome.tgz' -O data.transcriptome.tgz
tar -zxvf data.transcriptome.tgz

Data Processing

• Initial Transcriptome Assembly
• Symbiont Transcript Removal
• Clustering transcripts and counting assigned reads
• Functional Annotation with Trinotate
• Genotyping

Statistical Analysis and Visualisation

• Gene Annotation
• Differential Expression Analysis
• Analysis of Polyp Activity Observations
• Gene Function Analysis
• Relatedness
• Taxonomic Profiling of Raw Reads