Next Generation Sequencing Workshop
SEQUENCE READ ARCHIVE
The Next Generation Sequencing Workshop will include units covering the EBI's Sequence Read Archive (SRA) service. This is combined with an introduction to the ENA (European Nucleotide Archive), a section on data compression, and hands-on experience with SRA. 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.
RNA-Seq
Up and coming techniques to generate and analyse RNA-Seq data will be explored.
| Time | Topic |
|---|---|
| Day 1 - 12th March | |
| 09:00 - 09:30 | Shuttle bus from accomodation at Holiday Inn Express Duxford to EBI |
| 09:30 - 10:00 | Welcome, course registration and introduction |
| 10:00 - 11:00 | Speaker: Harold Swerdlow (Next-Generation DNA Sequencing: Current technology and future) |
| 11:00 - 11:15 | Tea/coffee break |
| 11:15 - 12:00 | Speaker: Aylwyn Scally (TBA: Assembly, alignments, variant calling) |
| 12:00 - 13:00 | Speaker: Jen Harrow (TBA: RGASP) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 14:30 | Speaker: Elizabeth Murchison (Sequencing the genome of the Tasmanian devil and its transmissible cancer) |
| 14:30 - 15:15 | RNA-Seq lecture (Simon White/John Collins) |
| 15:15 - 15:30 | Tea/coffee break |
| 15:30 - 16:00 | RNA-Seq practical (Simon White/John Collins) |
| 16:00 - 17:00 | Speaker: Jon Teague/ Adam Butler (Next Generation Sequencing applications in Human Cancer) |
| 17:00 - | Shuttle bus back to Holiday Inn Express Duxford |
| Day 2 - 13th March | |
| 08:30 - 09:00 | Shuttle bus from accomodation at Holiday Inn Express Duxford to EBI |
| 09:00 - 09:30 | ENA introduction (ENA team) |
| 09:30 - 10:00 | SRA introduction (ENA team) |
| 10:00 - 11:00 | SRA Submission, browsing, and data retrieval (ENA team) |
| 11:00 - 1115 | Tea/coffee break |
| 11:15 - 11:35 | Data compression (ENA team) |
| 11:35 - 12:15 | ENA submission (practical) |
| 12:15 - 13:15 | Lunch |
| 13:15 - 14:00 | ENA submission (practical) |
| 14:00 - 15:00 | Introduction to de novo assembly with Velvet (Matthias Haimel) |
| 15:00 - 15:15 | Tea/coffee break |
| 15:15 - 17:30 | Introduction to de novo assembly with Velvet (Matthias Haimel) |
| 17:30 | Shuttle bus back to Holiday Inn Express Duxford |
| Day 3 - 14th March | |
| 08:30 - 09:00 | Shuttle bus from accomodation at Holiday Inn Express Duxford to EBI |
| 09:00 - 09:45 | Speaker: Steven Wilder (ENCODE) |
| 09:45 - 10:15 | ChIP-seq anaylsis: lecture (Remco Loos and Myrto Kostadima) |
| 10:15 - 10:30 | Tea/coffee break |
| 10:30 - 13:00 | ChIP-seq practical: peak detection and peak annotation (Remco Loos and Myrto Kostadima) |
| 13:00 - 13:45 | Lunch |
| 13:45 - 15:30 | ChIP-seq practical: peak detection and peak annotation (Remco Loos and Myrto Kostadima) |
| 15:30 - 15:45 | Tea/coffee break |
| 15:45 - 16:30 | Speaker: Laura Clarke (1000 Genomes Project: a History, Methods and Results) |
| 16:30 - 17:00 | Course wrap-up and discussion |
| 17:00 | Shuttle bus back to Holiday Inn Express Duxford |
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
* A mini-bus from the Holiday Inn Express to and from the EBI each day
All delegates will need to arrange and pay for their own accommodation and travel to and from the EBI.
There will be a maximum of 38 participants on this course and participation is on a selection basis. Registration will close on 1st February 2012 @ 12:00 (midday) GMT. You will be notified by 6th February 2012 if you application has been successful.
To apply for this workshop please use the following link (Items marked * are mandatory. Incomplete registrations will not be processed).
Registration is now closed
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 book accommodation at the Holiday Inn Express, Whittlesford, Cambridge CB22 4NL. 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. If you wish to find alternative accommodation eg Cambridge, please see further information here : You will however have to make you own way directly to the EBI or the mini bus leaving from Whittlesford.