Next Generation Sequencing Workshop 2011
SEQUENCE READ ARCHIVE
The Next Generation Sequencing Workshop will include units covering the EBI's Sequence Read Archive (SRA) service. One day will be spent specifically on the SRA and the SRA will be used as the source for data to be processed in the other sessions. Students can expect to become familiar with submission and retrieval formats for both metadata and data, submission pipelines and data retrieval using browser and webservices methods.
VELVET / CURTAIN
Velvet and Curtain are two complementary tools that can be used for the assembly of genomes from next-generation sequence data. The session will consist of an introduction to both programs, followed by an exercise using short and long read data.
ChIP-SEQ DATA ANALYSIS
The goal of this session is to perform some basic tasks in the analysis of ChIP-seq data. We will find immuno-enriched areas using MACS and PeakAnalyzer utilities. We will visualize the data in a genome browser and perform annotation and motif analysis on the predicted binding regions.
| Times | Topic | Trainer |
|---|---|---|
| Tuesday 18 October 2011 | ||
| 09:30-10:00 | Registration and Tea/Coffee | |
| 10:00-10:15 | Welcome | |
| 10:15-10:45 | SRA Introduction (Rajesh Radhakrishnan) | |
| 10:45-11:15 | SRA: Browsing and Data retrieval (Marc Rosello) | |
| 11:15-12:00 | RNA-Seq in Ensembl, talk (Simon White) | |
| 12:00-13:00 | Lunch | |
| 13:00-13:30 | SRA: Submissions: SRA Webin (Arnaud Oisel) | |
| 13:30-14:00 | SRA: Submissions: SRA REST (Rajesh Radhakrishnan) | |
| 14:00-15:00 | SRA: Hands-on submissions and retrieval | |
| 15:00-15:15 | Tea/Coffee | |
| 15:15-17:00 | SRA: Hands-on submissions and retrieval | |
| Wednesday 19 October 2011 | ||
| 09:00-10:30 | Velvet / Curtain (Matthias Haimel) | |
| 10:30-10:45 | Tea/Coffee | |
| 10:45-13:00 | Velvet / Curtain (cont.) practical 1 practical 2 practical 3 |
|
| 13:00-13:45 | Lunch | |
| 13:45-14:30 | Cancer genomics: recent advances in sequencing and library prep technology (James Hadfield) | |
| 14:30-15:00 | Introduction to semiconductor sequencing / ion Community / Development Framework / Grand Challenges (Matt Dyer) | |
| 15:00-15:15 | Tea/Coffee | |
| 15:15-15:45 | Torrent Browser - Demo/Hands-on | |
| 15:45-16:15 | Plugin Development - Demo/Hands-on | |
| 16:15-16:30 | API - Demo/Hands-on | |
| 16:30-17:00 | Open time to explore and questions | |
| Thursday 20 October 2011 | ||
| 09:00-09:45 | modENCODE (Gos Micklen) | |
| 09:45-10:15 | Introduction to ChIP-seq Analysis, talk (Remco Loos) | |
| 10:15-10:30 | Tea/Coffee | |
| 10:30-13:00 | ChIP-seq Analysis (Hands-on), tutorial (Remco Loos) | |
| 13:00-13:45 | Lunch | |
| 13:45-14:30 | NGS in a Clinical Setting (Anthony Rogers) | |
| 14:30-16:00 | ChIP-seq Analysis (Hands-on) cont. (Remco Loos) | |
THIS COURSE IS NOW FULLY BOOKED
Registration Fees:
Registration Fee = £75.00
Please note that the registration fee includes:
* Meals at EBI (refreshments breaks and lunch)
* Course materials & USB stick
* Use of EBI IT Training Room computer during the 3 day course
All delegates will need to arrange and pay for their own travel to and from the course.
There will be a maximum of 38 participants on this course and registration is on a first come first serve basis. Registratio will close on 30 September 2011 @ 12:00 (midday) GMT.
To register for this workshop please use the following link (Items marked * are mandatory. Incomplete registrations will not be processed). You will need to pay by credit card as you submit your registration, therefore please have your card to hand.
Additional Information
This course will take place in the EMBL-EBI IT Training room which has 40 computers set up with the relevant disk images required for this course.
We recommend participants stay onsite and book accommodation at the Wellcome Trust Conference Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. We are provisionally holding some rooms at the WTCC under the name 'Holly Foster and Alison Barker', please quote this at time of booking. Your credit card details will be required in order to secure the booking. Rooms are limited and are on a first come first serve basis, therefore we recommend booking early.
Selected materials are available for download from the following link:
/training/sites/ebi.ac.uk.training/files/materials/2011/100806_ngs_edit.zip