Tutorial and training materials
ENCODE (Encyclopedia Of DNA Elements) is a big data consortium project that has for years generated huge amounts of important new data and analyses about various structural features and other aspects of genome organization. In this tutorial we will focus on the human and mouse data flowing into the UCSC Genome Browser via the Data Coordination Center (DCC) during the production phase of the project. Well describe the ENCODE portal that provides access to many project topics, and then move to exploring numerous data types in the Genome Browser. We will emphasize how to identify and locate data relevant to your research, and explore the data in the browser and other UCSC interfaces. Well examine visualization strategies and important track control features and track details. This tutorial assumes that the viewer has foundational knowledge of the UCSC Genome Browser and Table Browser tools. We also encourage viewers to access the consortiums publication: The ENCODE Project Consortium (2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol 9(4): e1001046. doi:10.1371/journal.pbio.1001046.
New: Explore the massive publication collection available on September 5 2012 via the ENCODE Explorer at Nature.
You will learn:
This tutorial is a part of the tutorial group Advanced Analysis and Queries. You might find the other tutorials in the group interesting:
BioMart: Management and querying of many types of biological data
UniProt: UniProt, Universal Protein Resource
DBTSS: Database of Transcriptional Start Sites
Galaxy: Analysis tools for researchers
This tutorial is a part of the tutorial group UCSC Tutorials. You might find the other tutorials in the group interesting:
ENCODE Foundations: ENCyclopedia of DNA Elements
UCSC Genome Browser: The Additional Tools: Additional tools at the UCSC Genome Browser
UCSC Genome Browser: Custom Tracks and Table Browser: UCSC Genome Browser advanced topics
UCSC Archaeal Genome Browser: Provides you with many research and analysis tools that can be used to examine the genomes of more than 50 microbial species from the domain archaea.
UCSC Genome Browser: An Introduction: The UCSC Genome Browser Introduction
Genome Databases (euk) : Genomic databases or repositories primarily aimed at eukaryotic organisms. Some may contain prokaryotic data as well.
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Spanking #ENCODE: While I was on the road last week--ironically to do workshops including one on ENCODE data in the UCSC Genome Browser, a conflama erupted over a new paper that was published essentially spanking the EN...
Updated ENCODE tutorial and training materials from OpenHelix once again freely available.: OpenHelix and the UCSC Bioinformatics group have worked together to give everyone free access to the newly updated ENCODE tutorial until the end of February 2013. The online tutorial suite teaches user...
New ENCODE track data available: On Friday I caught this announcement from the ENCODE mailing list. Fresh new data for your mining pleasure! Histone Modifications by ChIP-seq from ENCODE/University of Washington This track shows ge...
Recent BioMed Central research articles citing this resource
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