Statistical Methods for Next Generation Sequencing

Half-day course at ENAR 2012. Taught by
Zhijin (Jean) Wu [email: zwu@stat.brown.edu],
Kasper D. Hansen [email: khansen@jhsph.edu] and
Rafael A. Irizarry [email: rafa@jhu.edu]

Part of the course will be a hands-on lab session. This lab session will require a laptop with software installed prior to the course.

We will not have internet access and we will not have time to help with installation issues during the course.

The lab session will consists of three different parts

An overview of useful tools, lecture style
Hands on experience with an alignment program, Bowtie.
Performing a differential expression analysis using tools from Bioconductor on already summarized data.

In order to participate in part 2 or 3 you will need the following software installed.

Download and install R version 2.14.0 or newer 2. Download and install the latest version of Bowtie (don't confuse Bowtie with Bowtie 2 which is a different program). Note that it is possible to obtain binaries from the download page. It may be helpful to read the Getting started page. You will also need to download the index for S. Cerevisiae (CYGD). Put this index somewhere on your harddrive, according to the Bowtie instructions.
The following packages from Bioconductor: yeastRNASeq, GenomicRanges, cqn, edgeR, ShortRead. The package yeastRNASeq is big (about 300MB) and will only be used in the alignment portion of the lab session.

Install these R packages by starting R and then type

  R> source("http://www.bioconductor.org/biocLite.R")
  R> biocLite(c("edgeR", "cqn", "GenomicRanges", "yeastRNASeq", "ShortRead"))

yeastRNASeq contains a number of fastq files and Bowtie output. It may be easiest for you to locate these files and copy them to a more accessible location. You can locate these files by typing

  R> system.file("reads", package = "yeastRNASeq")

If you are on Windows, make sure you can unzip the gzip files.

Lectures