Whole Transcriptome Data Analysis

This is an introductory course with biologists as intended audience in mind. However basic knowledge of microarray technology and massively parallel sequencing (MPS) are desirable. The course participants will use open source Affymetrix and BioConductor software solutions; On the other side, R-coding skills and deep knowledge of statistics are not necessary for attendance because most analyses will be performed with OneChannelGUI (a graphical interface to a series of BioConductor tools prepared by Prof. R. Calogero, which enables handling microarray data analysis as well as secondary quantitative analysis of miRNA without requiring programming skills). Computers for hands-on exercises will be provided along with demo data sets, however, participants are welcome to bring along their own data to analyse.

Topics

Tools for microarray/RNA-seq data analysis

Experimental design

Quality control

Normalization and data reformatting

Basic Statistics

Selecting differentially regulated genes/microRNAs

Selecting alternative splicing events

Multiple testing

Biological interpretation



Aims of event

Understand the importance of experimental design in order to ask sensible biological questions

Assess the quality of your data

Perform normalization and reformatting procedures

Complete basic statistical tests on Next Generation Sequencing (NGS) data

Annotate and interpret your data and perform integration between gene-level expression and microRNA differential expression data

Understand some of the problems encountered when analysing data
+ show speakers and program

Day 1 - Wednesday, 27 June 2012 09:00 - 09:15 Course Introduction (Benes)
09:15 - 11:15 oneChannelGUI introduction, data loading, normalization, QC and data filtering at gene-level (Calogero)
11:15 - 11:35 Coffee break
11:35 - 13:00 Statistical detection and annotation at gene-level (Calogero)
13:00 - 14:00 Lunch
14:00 - 16:00 Gene-level exercise session
16:00 - 16:15 Coffee break
16:15 - 17:00 Exon-level analysis (Calogero)
Evening Dinner downtown Heidelberg



Day 2 - Thursday, 28 June 2012 09:00 - 10:00 About NGS sequencing technologies (Benes)
10:00 - 11:00 NGS primary mapping tools (Cordero)
11:00 - 11:30 Coffee Break
11:30 - 13:00 miRNA-seq: microRNA data analysis on oneChannelGUI, Statistical analysis of NGS data (Calogero)
13:00 - 14:00 Lunch
14:00 - 16:00 microRNA exercise session
16:00 - 16:30 Coffee Break
16:30 - 18:00 microRNA gene target detection (Calogero)



Day 3 - Friday, 29 June 2012 09:00 - 10:00 About alternative splicing analysis with RNA-seq (Cordero)
10:00 - 10:45 RNA-seq with oneChannelGUI (Calogero)
10:45 - -11:15 Coffee Break
11:15 - 13:00 RNA-seq exercise
13:00 - 14:00 Lunch
14:00 onwards Departure

25 Jun - 27 Jun 2013
Heidelberg
Germany
meeting website