Date:Tuesday 13 March 2018
Venue:European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
Application opens:Friday January 05 2018
Application deadline:Wednesday February 28 2018
Participation:First come, first served
This course will introduce users to the powerful search and retrieval methods available within ENA (European Nucleotide Archive) for annotated sequences, genomes, raw data and metadata, as well as download options from the ENA browser and an introduction to the various ENA browser tools.
There will also be a section on cross references and how to retrieve accessions for other resources linked to the primary data in ENA. There will be time at the end of the course for users to present their own use cases or request specific help for their own queries, enabling them to perform searches to enhance their own research.
We invite participants to bring along their use cases. These will serve to meet the expectations for attending the course. This course runs from 10:00 - 16:00 including breaks.
Please visit http://www.marinetraining.eu/ena-sequence-retrieval-workshop for full details of this event.
This workshop is aimed at any ENA user that regularly retrieves data from ENA or is planning to download large volumes of data in the near future. Bioinformaticians and other support staff who assist their teams/departments in data search and retrieval are also encouraged to attend. Part of the workshop will take the participants through a set of tools released by ENA in 2017 to greatly aid data download. For this component, knowledge of how to access the command line would be beneficial. Any user with existing data retrieval needs are encouraged to bring along their use cases for directed learning and assistance.
All participants should bring their own laptop, preferably with Python installed. We will be able to offer some assistance to the installation of Python if needed. Please indicate in your registration whether you are bringing a Window, Mac or Linux laptop.
Syllabus, tools and resources
The course will introduce users to:
- Advanced search and the ENA portal API
* Differences between the two
* Data portals and the API
* Building serach queries
* Metadata and sequence retrieval
- Downloading sequence data from the DNA browser
* Single and range accessions
* Download via taxon and/or project page
- Downloading run / analysis data
* Single accession from the browser (read and analysis tables)
* FTP vs Aspera
* ENA FTP downloader
- ENA browser tools
* Installation and setup
* Looking at the two tools and the options
* Downloading an assembly using enaDataGet
* Download an experiment using enaDataGet
* Downloading data for a study using enaGroupGet
* Downloading all sequences for a taxon using enaGroupGet
- Exploring links between ENA data
* Links between ENA data types
* Links from between ENA and other resources
- Specific use cases - discussion and assistance