Ensembl gene annotation workshop

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Do you want to annotate genes and transcripts of your favourite genome?
Will you be in Cambridge (UK) for the Genome Informatics 2014 meeting?
Have you worked with the Unix command line?

ebang-60If your answer is yes to any of the above, you may want to attend our ‘Introduction to Ensembl automatic gene annotation’ workshop on 19-20th of September 2014. Registration is free, but participants need to cover their own accommodation, sustenance and transport expenses.

THIS COURSE IS NOW FULL. Registration is closed.

The workshop

Dan and Fergal from the Ensembl Genebuild team will show how to create your own core database for genome annotation, load a genome assembly and run some of the analyses using the Ensembl genebuild system.

Pre-requisites

Unix (or Linux) knowledge is mandatory. Participants are also expected to have some knowledge of relational databases (e.g. MySQL) and object-oriented programming (the Ensembl API uses Perl).

Topics

  • Introduction to the Ensembl genebuild system, including data input types, how to generate protein-coding transcript models, and add UTR to these models
  • Introduction to assembly structure (toplevel, contigs, scaffolds,  chromosomes)
  • Core database schema
  • Tracking jobs in the system
  • Runnable and RunnableDB modules

Practical sessions

  • Creating a genebuild database
  • Loading an assembly into the database
  • Running algorithms first on the commandline and then using the  pipeline
  • Understanding how the pipeline code interacts with the algorithms and the database
  • Understanding the pipeline’s job tracking system
  • Visualisation of results with Apollo

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Genomics Informatics 2014

Our Ensembl Gene Annotation workshop will precede this year’s Genome Informatics conference taking place in Cambridge (UK) on 21-24th September.

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Please click here for more details on Genome Informatics 2014, including deadlines and programme.