Jul 14, 2014

HTS data analysis course


The Oslo node of the ELIXIR Norway Bioinformatics Platform (Bioinformatics Core Facility), the Oslo node of the Norwegian Genomics Consortium (Genomics Core Facility) and the Norwegian Sequencing Centre are happy to invite you to an introductory hands-on course on analysis of next-generation sequencing data using bioinformatics tools. This course is partly administered by the Department of Informatics at the University of Oslo, and can thus give credits to PhD and master students (see below).

Registration deadline: Aug 28, or alternatively Aug 14 for PhD and master students (see below).

Time and place: Sept 22 and Oct 6 - Oct 24, 09:00 AM to 05:00 PM, four days each week (with most likely Fridays off).

The High Throughput Sequencing technologies and bioinformatics analysis course consists of three weeks of lectures and practicals plus reading materials. Two weeks before the main course, on Sep 22, a UNIX pre-course will be given. UNIX knowledge is essential for participation in the main course.

The course is free of charge, and registration is required (30 participants in total, for which 15 are reserved for students taking the course for credit). No accommodation or meals provided.

Prerequisites:

All participants should have a basic understanding of molecular biology, at least roughly corresponding to 5-10 university study points in molecular biology, biochemistry, or similar. If you are uncertain if your biology background is strong enough, please contact the course coordinators before signing up for the course.

No prior background in bioinformatics or computer science is required, however, we expect students to have a basic understanding of the UNIX shell. Participants without this knowledge have to take the introductory UNIX course on Monday September 22nd - details will be provided upon acceptance of registration.

The following topics will be covered:

- Introduction to various next-generation sequencing platforms and data formats;
- Quality and quantity control of sequencing data;
de novo genome assembly of DNA-seq reads;
- Analysis of data from small RNA and mRNA sequencing projects;
- Variant calling and annotation of SNPs;
- Basic and applied use of LifePortal/Galaxy and the Genomic Hyperbrowser tools.

Instruction and hands-on exercises are planned from 9:00 to 17:00 every day. Participants are expected to attend the complete course. A detailed schedule will be provided later, in a follow-up e-mail addressed to all confirmed participants.

Teaching will take place in a computer lab with preinstalled computers. It is not necessary to bring a computer.

Applying:

To keep the course as interactive as possible, we are limiting the number of participants. We therefore ask that each institution/group only apply for one person.

Please apply for the course by registering before 28th of August at this link. Feedback on participation will be given on or soon after September 5th. (Soon to be) active users of the organising platforms will be given priority.

More information about the course:

Click here to find the wiki page for the course.

To master/PhD students:

Please note that this course is also available as a university course at both master (INF-BIO5121) and PhD level (INF-BIO9121), in either case for 10 study points. Contact your study administration if you have more questions about how to register for the university course.

Please register to one of the following courses:

PhD course (10 study points) INF-BIO 9121. NOTE the website is not up yet, and registration may not work. Please contact studieinfo@ifi.uio.no for more information.

Master level course (10 study points) INF-BIO5121. NOTE the website is not up yet, and registration may not work. Please contact studieinfo@ifi.uio.no for more information.

NOTE that the deadline for registering to the course as a credit student at UiO is August 14th.

 
 
 
 
 
 


News

Jan 18, 2018

Due to a resent hacker attack to the OUS IT system, we currently are unable to receive or send emails to the rr-research domain. Until further notice please use this email to contact us “genomics.cf.oslo@gmail.com”

Feb 24, 2016

The HiSeq 4000 build upon the existing HiSeq 2500 platform using the new HiSeq X patterned flow cell technology, providing unparalleled speed and performance. The dual-flow cell HiSeq 4000 System delivers the highest throughput and lowest price per sample across multiple applications. The new sequencer will provide users will faster turnaround time (run time is 3 days compared to 6-11 days in HiSeq 2500) and higher quality, more data per run and longer reads (150 bp paired-end).


Contact Information:

genomics.cf.oslo@gmail.com

Visiting address:
Genomics Core Facility (Room 3-F8-04)
Department of Core facilities
Institute for Cancer Research
New OCCI-building 
 
Norwegian Radium Hospital 
Ullernchaussen 66, Lamell 3, 2B 
NO-0379 Oslo, NORWAY

+47 - 9183 2772 Laboratory
+47 - 9183 3425 Office

Daily Leader Core Facility
Susanne Lorenz, PhD

Head of Core Facility
Leonardo A. Meza-Zepeda, Dr. philos.

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