GLBio RNA-Seq Workshop

This is the main repository for the RNA-Seq hands-on workshop, held at GLBio 2015, Purdue University. During this workshop, you will learn the basics of RNA-Seq data analysis, focusing on quality control, sequencing read alignment, and differential expression analysis.

This course assumes a very basic knowledge of Linux, R, and next-generation sequencing (NGS). All materials in this course are free and open; feel free to reuse them as you like.

Please find all workshop instructions on the workshop wiki page.

Description of Datasets and Tools Used in the Workshop

Datasets

Name	Download link	Local path	Description
Quality-Control Example Dataset	Link	./datasets/BodyMap	Small samples of datasets from the Illumina BodyMap 2.0 project; specifically, the datasets are paired-end 50bp reads from adrenal and brain tissues. The sampled reads map mostly to a 500Kb region of chromosome 19, positions 3-3.5 million (chr19:3000000:3500000)
RNA-Seq Analysis Dataset	NA	./datasets/workshop	Simulated data from human chromosome 21. 1-2M reads are simulated with various parameters, including length and mutation rates. Samples are paired-end, with 3 treatment and 3 controls.

Tools

Name	Download link	Local path	Description
FastQC	Link	./tools/FastQC	A quality control tool for high throughput sequence data
Trimmomatic	Link	./tools/Trimmomatic	Performs a variety of useful trimming tasks for Illumina paired-end and single-end data. The selection of trimming steps and their associated parameters are supplied on the command line.
Bowtie2	Link	./tools/bowtie	An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
SAMtools	Link	./tools/samtools	Provides various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
TopHat	Link	./tools/tophat	TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Cufflinks	Link	./tools/cufflinks	Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

Aknowledgement: Matterials of NGS course and Next Generation Data Analysis Marathon are used to develop the contents of this workshop. Please visit the main websites for more information on RNASeq data analysis, as well as additional NGS data analysis pipelines.