Browsing Genes and Genomes with UCSC: Basic Workshop

Course date: 01 April 2015 - 01 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 basic course. Participants here will have the possibility of gaining lots of hands-on experience in the use of the UCSC genome browser and also be provided with the necessary background information.

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).

Course summary
This workshop will show how the UCSC Genome Browser is used to view multiple data sets at a variety of scales, from single-base to whole-genome. Attendees will learn browser navigation and an overview of the paradigm for data display. Selected datasets will be presented, such as UCSC Genes (a gateway to a large number of data sources) OMIM and Comparative Genomics tracks. Attendees will also learn about search, and about sharing information with others via Custom Tracks, the Sessions tool and the pdf-export function. Also presented will be the most recent tools, including bigBed and bigWig file formats, display of BAM files from high-throughput sequencing and data hubs.
Practical exercises will include Table Browser queries; using Custom Tracks; BLAT, a program for sequence alignment on the genome and the isPCR tool to test the uniqueness and predicted product from PCR (including on RNAs).
Attendees are encouraged to come with questions/problems.

The only prerequisite for this workshop is general knowledge of molecular biology/ genomics and a familiarity with web browsers.

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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