Genome management and analysis with CoGe

With over 23,000 genomes from 17,000 different organisms, CoGe is where most people are managing and analyzing their genomic data. This two hour workshop will provide in-depth, hands-on training: Managing your genome in CoGe: How to add your own genome to CoGe, add structural and functional annotations, keep it private, share it with collaborators, and make it fully public (http://genomevolution.org/r/8kzz) Integrating functional and diversity data: The EPIC-CoGe addition enables researchers to integrate RNASeq, BS-Seq, ChIP-Seq, DNA resequencing data, microarrays, and any other type of quantitative genomic measurements to any genome in CoGe (http://genomevolution.org/wiki/index.php/EPIC-CoGe_Tutorial) Map NGS reads to a genome: EPIC-CoGe’s RNASeq processing and SNP discovery pipelines make it easy to transform you read data into quantitative measurements. (https://www.youtube.com/watch?v=3fNyHGB02dM) Visualizing your genomic data: The EPIC-CoGe genome browser, based on JBrowse, is instantly available for any genome and associated data loaded into CoGe (http://genomevolution.org/r/9xjy) Whole genome comparisons: Identify and classify orthologous and paralogous genes, identify whole genome duplications, use synteny to order and orient contigs and scaffolds against any reference genome to create pseudo-assemblies Micro-synteny analyses: Identify gene model errors, conserved non-coding sequences, tandem gene duplications, and changes in local genome structure Multiple whole genome synteny analyses: Given a gene in one genome, find syntenic regions across multiple genomes, even if that specific gene is not present. CoGe offers a multitude of advanced on-the-fly analyses. To accomplish these, CoGe is part of the Powered by iPlant Program and leverages iPlant’s Cyberinfrastructure for computational scalability. Learn more about this program at: http://www.iplantcollaborative.org/discover/powered-by-iplant
Date: Saturday, January 10, 2015
Time: 4:00 PM-6:10 PM
Room: California
Eric Lyons
Haibao Tang and Eric Lyons
4:00 PM
Genome Analysis with CoGe
Haibao Tang, University of Arizona

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