This is the website for workshop WS-C-2, part of the DevCom project.
This workshop will address the logistical difficulties and complexities of analysing data derived from next-generation, high throughput sequencing technologies. It will concentrate on the essence of the methods, and useful tools, for the extraction of useful information from the primary sequence data, as well as the practical difficulties of handling very large data sets. It will also look at the statistical underpinnings of the analysis of this type of data, and try and clarify the uncertainties in the current methods. The course will cover analysis of RNA-seq data, both differential expression and time series, and ChIP-seq data, both for sequence-specific transcription factors and for broader chromatin marks.
Simon van Heeringen - Mol. Dev. Biology, Radboud University Nijmegen
Mike Gilchrist - MRC National Institute for Medical Research
The tentative schedule of the workshop is shown below. The specifics are subject to change.
| Time | Contents |
|---|---|
| 8:30 - 9:00 | Welcome & coffee |
| 9:00 - 10:00 | Introduction to next-generation sequencing |
| 10:00 - 12:00 | Shell tutorial |
| 12:00 - 13:00 | Lunch |
| 13:00 - 18:00 | BAM, samtools, FASTQ |
| Time | Contents |
|---|---|
| 8:30 - 8:45 | Coffee |
| 8:45 - 9:45 | Introduction to ChIP-seq |
| 9:45 - 12:00 | Mapping and peak calling |
| 12:00 - 13:00 | Lunch |
| 13:00 - 14:30 | Introduction to RNA-seq |
| Time | Contents |
|---|---|
| 8:30 - 8:45 | Coffee |
| 8:45 - 12:30 | RNA-seq |
| 12:30 - 13:30 | Lunch |
| 13:30 - 14:30 | Seminar Mike Gilchrist |
| Time | Contents |
|---|---|
| 8:30 - 8:45 | Coffee |
| 8:45 - 10:00 | Analysis of ChIP-seq data |
| 10:00 - 12:00 | Intersections, Clustering and profiles |
| 12:00 - 13:00 | Lunch |
| 13:00 - 18:00 | Motif analysis |