Browsing Genes and Genomes with UCSC: Advanced Workshop

Course date: 02 April 2015 - 02 April 2015
Location: Erasmus MC, OWC-22

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The Erasmus Postgraduate School Molecular Medicine organizes a series of courses and workshops on Bioinformatics.
We organize two one-day workshops on the use of the UCSC genome browser: one basic course and one advance course. This is the advanced course.

This workshop will be given by Dr. Robert Kuhn of the UC Santa Cruz, California, U.S.A.

Course Schedule
Each course will take up one day and will include practical sessions.

The course starts at 9.30 and ends at 17.00.
Coffee break 10.45 - 11.00
Lunch break 12.30 - 13.30
Coffee break 14.45 - 15.00

It will be held in computer room 22 at the Erasmus MC Educational Center (OWC).

Program summary
A brief review of recent innovations in navigation will be presented, as well as a deeper look at the SNP datasets, structural variation tracks and others, especially Comparative Genomics tracks, analysis of high-throughput sequencing data and the Variant Annotation Integrator. 
The new Genome Browser-in-a-Box, a UCSC intstance that runs on your desktop, next to sensitive data, will be discussed.

The Practicum will include advanced Table Browser queries, including filters and intersections between native tracks and custom tracks.
Advanced use of Custom Tracks will include control of display parameters, including colors, etc. Custom Track display of high-throughput sequencing data will be also be addressed: BAM and VCF files, Personal Genome SNP format.

Prerequisites: Beginner workshop or basic familiarity with the Genome Browser.

Attendees are encouraged to come with questions.

Participation in this course equals 0,4 ECTS

Registration fee
The fee of non-commercial participants for this course is 200.
If you also participate in the advanced course, the total fee is 350.

Discounts are handled as follows:

  • All participants from the postgraduate school MolMed receive a discount of 100% and pay 0.
  • All PhD students get a discount of 50% and pay 100/175.
  • Other Erasmus MC participants, like MGC, NIHES members, and master students from elsewhere get a discount of 50% and pay 100/175.
  • Master students from elsewhere who pay the fee from their personal budget get a discount of 75% and pay 50/87,50.
  • MGC-Erasmus MC members receive 100% discount if they follow both the basic and the advanced course.


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