Advanced RNA-Seq and ChiP-Seq data analysis
EMBL Heidelberg, Germany Monday 7 June - Wednesday 9 June 2010
Programme
Preliminary Programme
| Monday, 7 June 2010 09.00 - 17.30 | |
|---|---|
| 09.00 - 09.20 | Welcome and Introductions Wolfgang Huber |
| 09.20 - 10.00 | EMBL GeneCore and its next generation sequencing services Vladimir Benes |
| 10.10 - 11.00 | Overview of R/Bioconductor packages for short read analysis Martin Morgan |
| 11.00 - 11.15 | Coffee Break |
| 11.15 - 12.00 | Recent developments in short read alignment. Tobias Rausch |
| 12.00 - 13.30 | Lunch |
| 13.30 - 14.20 | R/Bioconductor I/O (ShortRead) Martin Morgan |
| 14.30 - 15.20 | IRanges & Biostrings Patrick Aboyoun |
| 15.20 - 15.40 | Coffee Break |
| 15.40 - 17.30 | Practical session 1: Reading and manipulating short reads Starting from SAM file, visualise alignments and coverage vectors, make quality-related plots. |
| Tuesday, 8 June 2010 09.00 - 17.30 | |
|---|---|
| 09.00 - 09.50 | Annotation Patrick Aboyoun |
| 10.00 - 10.50 | Differential expression Simon Anders |
| 10.50 - 11.10 | Coffee Break |
| 11.10 - 12.00 | Practical session 2: RNA-Seq: producing a feature count table |
| 12.00 - 13.00 | Lunch |
| 13.00 - 15.15 | Practical session 2: RNA-Seq: producing a feature count table |
| 15.15 - 15.30 | Coffee Break |
| 15.30 - 16.20 | ChIP-seq analysis of sequence-specific factors with SWembl Petra Catalina Schwalie |
| 16.30 - 17.20 | MACS, CisGenome, SISSRs and other peak calling algorithms: differences and practical use Charles Girardot |
| Wednesday, 9 June 2010 09.00 - 15.00 | |
|---|---|
| 09.00 - 09.50 | The specific data analysis issues in applications to microRNA discovery Paul Bertone |
| 10.00 - 12.00 | Practical session 3: ChIP-Seq |
| 12.00 - 13.00 | Lunch |
| 13.00 - 14.30 | Higher level analysis & advanced topics: |
| 13.00 - 13.30 | Essential statistical building blocks: lm, glm, *nbinom and other distributions, p.adjust; MLInterfaces for clustering and classification |
| 13.30 - 14.00 | Multiple testing, FDR, (pseudo-)ROC curves, non-specific filtering |
| 14.00 - 14.30 | Integrative analysis: handling metadata; gene and genome coordinates; advanced graphics: lattice; gWidgets / RGtk2; rgl |
| 14.30 - 15.00 | Wrap up, Q&A, feedback |