Amplicon Sequencing

Lecture notes

Amplicon Sequencing

Get Ready for the exercises

For the exercises you need to download and unzip the R script, the data, and some "homebrew" functions. All files are combined in one zipped file. Below are all the steps in R you need to download, unzip, and open the R script. Have fun!

## You need this R library to use wget
library("HelpersMG")

## Working directory
getwd()

## Create a new working folder
dir.create("/your/path/AmpSeq/") # please change it accordingly

## Change to new working directory
setwd("/your/path/AmpSeq/")

## Confirm ne working directory
getwd()

## Download the zipped exercise files
wget("http://gdc-docs.ethz.ch/GeneticDiversityAnalysis/GDA19/data/AmpSeq.zip")

## Unzip the data
unzip("AmpSeq.zip") 

## Have a look at the folder content
list.files(getwd())
# These are the files you should see in your working directory:
# (1) AmpSeq.zip: your original data file 
# (2) AmpSeqExercises.R: R script
# (3) Chaillou2015.Rdata: input file
# (4) graphical_methods.R: file with various functions 

## Load R script
file.edit("AmpSeqExercises.R")

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Data Analysis

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