Next Generation Sequencing Workshop
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. Procedures learned in the course can be extended across species. Mouse data will be used in this tutorial.
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.
ASSEMBLY, RESEQUENCING, AND VARIANT CALLING
Assembly of genomes from next-generation sequencing data, resequencing and variation calling using Velvet, Newbler, SAM, and others. The session will consist of an introduction, followed by hands-on exercises.
RNA-Seq
Up and coming techniques to generate and analyse RNA-Seq data will be explored. Procedures learned in the course can be extended across species. Zebrafish data will be used in the tutorial.
| Time | Topic |
|---|---|
| Day 1 - Tuesday 16 October 2012 | |
| 09:00 | Registration and coffee |
| 09:30 - 10:30 | Introduction (Karim Gharbi, GenePool, Edinburgh) Presentation |
| 10:30 - 11:00 | ChIP-Seq analysis: Lecture (Remco Loos/Myrto Kostadima) |
| 11:00 - 11:15 | Coffee/Tea |
| 11:15 - 13:30 | ChIP-seq analysis: Practical (Remco Loos and Myrto Kostadima) |
| 13:30 - 14:30 | Lunch |
| 14:30 - 16:00 | ENA/SRA (Guy Cochrane, Rajesh Radhakrishnan, Marc Rossello, Arnaud Oisel |
| 16:00 - 16:15 | Coffee/Tea |
| 16:15 - 17:30 | ENA/SRA (Guy Cochrane, Rajesh Radhakrishnan, Marc Rossello, Arnaud Oisel |
| Day 2 - Wednesday 17 October 2012 | |
| 9:00 - 11:00 | Resequencing, variant calling, and assembly (Timothee Cezard and Karim Gharbi, GenePool, Edinburgh) genome_assembly-tutorial.pdf, reseq_wrkshop.pdf, reseq-wrkshp.pptx, reseq_wkshp2.ppt, reseq_wrkshp2-2.pdf, variant_calling-tutorial.pdf |
| 11:00 - 11:15 | Coffee/Tea |
| 11:15 - 13:00 | Resequencing, variant calling, and assembly (Timothee Cezard and Karim Gharbi, GenePool, Edinburgh) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:00 | Resequencing, variant calling, and assembly (Timothee Cezard and Karim Gharbi, GenePool, Edinburgh |
| 15:00 - 15:45 | 1000 Genomes Project (Laura Clarke) |
| 15:45 - 16:00 | Coffee/Tea |
| 16:00 - 17:00 | Comparative cancer genomics (Elizabeth Murchison - The Sanger Institute) |
| Day 3 - Thursday 18 October 2012 | |
| 09:00 - 10:45 | RNA-Seq lecture and practical - (John Collins, Bronwen Aken, Thibaut Hourlier) |
| 10:45 - 11:00 | Coffee/Tea break |
| 11:00 - 13:00 | RNA-Seq Lecture and practical - (Myrto Kostadima/Remco Loos) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:30 | Cancer Genomics - (Adam Butler, Simon Forbes, Jon Teague) |
| 15:30 - 16:15 | Coffee/Tea break |
| 16:15 - 17:00 | Course Wrap-up |
Registration Fees:
Registration Fee =£90.00
Please note that the registration fee includes:
* Meals at EBI (refreshments breaks and lunch)
* Dinner at the 'Red Lion Pub, Hinxton' - (Tuesday 16 October 2012)
* Course materials & USB stick
* Use of the EBI IT Training Room computer during the 3 day course
All participants will need to arrange and pay for their own accommodation and travel to and from the EBI.On-campus accommodation is available (see below).
Application for this event will close on Wednesday 29 August 2012 @ 12:00 (midday) GMT.
To apply for this workshop please use the following link (Items marked * are mandatory. Incomplete registrations will not be processed).
Applicants will be notified if they have been successful shortly after the closing date.
Application 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.
Shortly after the closing date, the successful applicants will be sent the link to register and make the payment for this event. Applicants can then book their accommodation.
We recommend that participants book accommodation at Hinxton Hall (Situated onsite at the Genome Campus, Hinxton). We have reserved a number of rooms onsite, and if you would like to book a room, please mention code '1815/NGS Course' at the time of booking.
Please note: Accommodation at Hinxton Hall will only be held until Friday 31 August 2012.
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 you book 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.