<commit_before>---
layout: post
title: "NERC Exeter: Metagenomics three hour practical"
description: ""
category: 
tags: []
---
{% include JB/setup %}

##Whole-genome shotgun metagenomics learning objectives

- Know how to subsample reads from a FASTQ file without losing paired-information (20 minutes)
- Know how to perform basic taxonomic assignment using a marker-gene method: MetaPhlan (10 minutes)
- Assess the impact sampling has on discovery of taxa (20 minutes)
- Know how to use MEGAN to visualise taxonomic information (30 minutes)
- Understand how the Lowest Common Ancestor parameters affect sensitivity and specificity of taxonomic assignments (20 minutes)
- Know how to use MEGAN to visualise functional information (30 minutes)
- Understand how to compare multiple samples in MEGAN (30 minutes)

###Optional, more advanced objectives (if you finish, or when back at home)
- Know how to generate a heatmap of taxa from Metaphlan results (20 minutes)
- Assemble a metagenome with Velvet (30 minutes)
- Know how to perform basic taxonomic and functional assignment using a sequence similarity method: BLAST/RapSearch2 (10 minutes)

#Part I: Multivariate statistics tutorial

- Login to Amazon cloud and start a new Terminal
- Get the tutorial from my Dropbox:

	wget <https://dl.dropboxusercontent.com/u/7163977/MultivariateStats.tar.gz>

- Go into Tutorials, untar the archive and cd into it:

	tar xvfz MultivariateStats.tar.gz
	
	cd MultivariateStats
	
- Download the tutorial slides from and follow the steps:

    <http://nickloman.github.io/static/MultivariateStatsTutorial.pdf>

# Part II: Taxonomic assignments from metagenomics data
##Datasets for this practical

For this practical we will use some real clinical metagenomics data from the E. coli outbreak in 2011, published in this JAMA article: <http://jama.jamanetwork.com/article.aspx?articleid=1677374>

*List* the contents of the the ~/shotgun\_metagenomics/ directory (remember ~ is just a short-cut for your home directory, e.g. /home/ubuntu, so this is the same as /home\/ubuntu/shotgun_metagenomics).

Q1. What format are the reads, and what can you deduce about the sequencing from them?

Q2. How many reads are in the biggest and the smallest files?<commit_msg>tutorial<commit_after>---
layout: post
title: "NERC Exeter: Metagenomics three hour practical"
description: ""
category: 
tags: []
---
{% include JB/setup %}

##Whole-genome shotgun metagenomics learning objectives

- Know how to subsample reads from a FASTQ file without losing paired-information (20 minutes)
- Know how to perform basic taxonomic assignment using a marker-gene method: MetaPhlan (10 minutes)
- Assess the impact sampling has on discovery of taxa (20 minutes)
- Know how to use MEGAN to visualise taxonomic information (30 minutes)
- Understand how the Lowest Common Ancestor parameters affect sensitivity and specificity of taxonomic assignments (20 minutes)
- Know how to use MEGAN to visualise functional information (30 minutes)
- Understand how to compare multiple samples in MEGAN (30 minutes)

###Optional, more advanced objectives (if you finish, or when back at home)
- Know how to generate a heatmap of taxa from Metaphlan results (20 minutes)
- Assemble a metagenome with Velvet (30 minutes)
- Know how to perform basic taxonomic and functional assignment using a sequence similarity method: BLAST/RapSearch2 (10 minutes)

#Part I: Multivariate statistics tutorial

- Login to Amazon cloud and start a new Terminal
- Get the tutorial from my Dropbox:

	wget <http://nickloman.github.io/static/MultivariateStats.tar.gz>

- Go into Tutorials, untar the archive and cd into it:

	tar xvfz MultivariateStats.tar.gz
	
	cd MultivariateStats
	
- Download the tutorial slides from and follow the steps:

    <http://nickloman.github.io/static/MultivariateStatsTutorial.pdf>

# Part II: Taxonomic assignments from metagenomics data
##Datasets for this practical

For this practical we will use some real clinical metagenomics data from the E. coli outbreak in 2011, published in this JAMA article: <http://jama.jamanetwork.com/article.aspx?articleid=1677374>

*List* the contents of the the ~/shotgun\_metagenomics/ directory (remember ~ is just a short-cut for your home directory, e.g. /home/ubuntu, so this is the same as /home\/ubuntu/shotgun_metagenomics).

Q1. What format are the reads, and what can you deduce about the sequencing from them?

Q2. How many reads are in the biggest and the smallest files?
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{'dir': 'git-commits-cleaned', 'id': '974293', 'n_tokens_mistral': 1338, 'n_tokens_neox': 1182, 'n_words': 583}