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Encode RNA Dashboard

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The ENCODE project has produced a massive amount of transcriptome data, made possible by the collaboration of a world wide consortium of laboratories. During the project it was critical to immediately …

The ENCODE project has produced a massive amount of transcriptome data, made possible by the collaboration of a world wide consortium of laboratories. During the project it was critical to immediately know what data was being produced by which lab. The ENCODE RNA dashboard kept the researchers informed about new results, even before they were officially registered with the ENCODE Data Coordination Center (DCC). It was instrumental for management to have direct insight into the current state of the project at any given point in time. Collaborators could quickly proceed with their own analysis steps once the raw data and processed results were published on the dashboard by other groups. The dashboard was also enriched with direct links to additional summary statistics that had been published using the Grape RNA-Seq pipeline.
Now that the project has yielded its results, the ENCODE dashboard still remains the only central place collecting all the RNA data produced by the ENCODE project. The international research community can explore the wide range of experiments, and quickly find and download the exact data sets they need for their own data analysis. The dashboard is not only useful for web access, but command line users will enjoy the friendly batch processing capabilities.
There is a huge demand to provide the same kind of dashboard for additional ENCODE projects, and with the new version of our dashboard software package, the system can even be extrapolated to any other bioinformatics project having to deal with a lot of data. For example, the ENCODE Mouse (Mus musculus) dashboard is one of the upcoming dashboards, replicating the success of the ENCODE hg19 (Homo sapiens) dashboard.

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  • 1. ENCODE RNA Dashboard HUB5 - Heidelberg 21. March 2013 Maik Röder Python Consultant roeder@berg.net http://genome.crg.es/ encode_RNA_dashboardThursday, March 21, 13
  • 2. ENCODE RNA Dashboard • The ENCODE project has produced massive amount of transcriptome data • How to keep up to date during production, even before submission to the ENCODE Data Coordination Center (DCC)? • Direct links to additional summary statistics produced by the Grape RNA-Seq pipelineThursday, March 21, 13
  • 3. USCS Genome Browser - ENCODE • First, a look at the current UCSC genome browser Experiment Matrix for ENCODE • http://genome.ucsc.edu/ ENCODE/Thursday, March 21, 13
  • 4. ENCODE Experiment Matrix (UCSC) Files RNA-SeqThursday, March 21, 13
  • 5. Search + List (UCSC)Thursday, March 21, 13
  • 6. Mouse Experiment Matrix (UCSC)Thursday, March 21, 13
  • 7. Search + List (UCSC)Thursday, March 21, 13
  • 8. ENCODE RNA dashboard • http://genome.crg.es/encode_RNA_dashboard/hg19/ • Summary of transcriptome data production • Overview • Exploration • Batch DownloadThursday, March 21, 13
  • 9. ENCODE RNA Dashboard Human (hg19) ExplorationThursday, March 21, 13
  • 10. Exploration Click to make file details appear in place Click again to make list disappear and continue exploringThursday, March 21, 13
  • 11. ENCODE RNA Dashboard Mouse (mm9)Thursday, March 21, 13
  • 12. ExplorationThursday, March 21, 13
  • 13. Batch Download • http://genome.crg.es/ encode_RNA_dashboard/HOWTO_batch- download.htmlThursday, March 21, 13
  • 14. Today • ENCODE dashboard still remains the only central place collecting all the RNA data produced by the ENCODE project • The international research community can explore the wide range of experiments • Quickly find and download the exact data sets they need for their own data analysis. • command line users will enjoy the friendly batch processing capabilitiesThursday, March 21, 13
  • 15. Upcoming • Dashboard generation tool • Reimplementation in Python using Pandas • Methods Paper to be published soonThursday, March 21, 13
  • 16. Thanks • This work has been supported by the Centre for Genomic Regulation (CRG) in Barcelona • Roderic Guigó • Julien Lagarde • Learn about Pandas at the Python Meetup: • Monday, April 15th • http://www.meetup.com/HeidelbergPythonThursday, March 21, 13

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