2011 advanced RNA-seq course

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Organization and Logistics

This is course is organized by Peter-Bram 't Hoen (LUMC), Johan den Dunnen (LUMC), Celia van Gelder (NBIC/BioWise), Antoine van Kampen (AMC). The course is hosted at Amsterdam Medical Centre.

Program & course material

Day 1 08/25/11 '
Time Activity Speaker / Practical Supervisor
9:00 – 9:30 Registration
9:30 – 10:15 Introduction to RNA-seq technology and sample preparation protocols Peter-Bram ‘t Hoen (LUMC)
10:15 – 10.45 RNA-PolII ChIP-seq and epigenomics Nagesha Rao (RUN)
10:45 – 11.00 Coffee Break
11.00 – 11.30 Alignment tools for RNA-seq data (I) Marieke Simonis (UMCU)
11.30 – 12.00 Alignment tools for RNA-seq data (II) Kai Ye (LUMC)
12:00 - 13:00 Lunch
13.00 – 13.30 Overview of R/Bioconductor packages for short read analysis Philip de Groot (WU)
13:30 - 15:30 Practical: Reading and manipulating short reads starting from SAM file, visualize alignments and coverage vectors, make quality-related plots Marieke Simonis (EMC) / Philip de Groot (WU)
15:30 - 15:45 Coffee Break
15:45 – 16:15 Quality control Peter-Bram ‘t Hoen (LUMC)
16.15 – 16.45 Biases in RNA-seq data Antoine van Kampen (AMC)
Day 2 08/26/11 '
9:00 – 9:45 Statistical tests for differential expression in count data (I) Erik van Zwet (LUMC)
9.45 – 10.30 Statistical tests for differential expression in count data (including pathway testing) Jelle Goeman (LUMC)
10:30 - 10:45 Coffee Break
10:45 – 11:00 Introduction R packages baySeq, edgeR, DESeq Peter-Bram ‘t Hoen (LUMC)
11.00 – 12.00 Practical baySeq / DEseq Rutger Brouwer (EMC), Marcel Willemsen (AMC), Peter-Bram ‘t Hoen (LUMC)
12:00 – 13:00 Lunch
13:00 – 14.00 Practical edgeR Peter-Bram ‘t Hoen (LUMC) / Rutger Brouwer (EMC)
14.00 – 14.45 Allele-specific expression Hendrik Marks (RUN)
14.45 – 15.30 eQTL analysis Harm-Jan Westra (UMCG)
15:30 – 15.45 Coffee Break
15.45 – 16:30 How to store and visualize RNA-seq data Gabriella Rustici (EBI)
16.30 – 17.00 Questions and answers