PATRIC Workshop – San Diego State University

Published on 2015-07-14

AGENDA

Monday, July 20, 2015

9:30am            Register for PATRIC Account

10:00am          Overview of PATRIC (http://www.patricbrc.org/) – Tom Brettin

10:30am          Assemble a Genome in PATRICBob Olson

  • Uploading reads and read libraries
  • Selecting assembly methods for comparison
  • Queuing jobs and retrieving results
  • Analyzing assembly output and comparisons
  • Genome assembly

11:00am          *Break*

11:15am          Annotate a Genome in PATRIC Using RASTtk – Bob Olson

  • Uploading or selecting contigs in workspace
  • Selecting genome metadata and annotation options
  • Queuing jobs and retrieving results
  • Previewing an annotated genome
  • Genome Annotation

12:00pm          *Lunch*

1:00pm            Metabolic Modeling in PATRIC – Jim Davis

2:00pm            Proteomic Comparison – Jim Davis

  • Selecting genomes for a study
  • Visualization of compared genomes
  • Download and analysis of results
  • Proteome Comparison

3:45pm            Adjourn

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Tuesday, June 21, 2015

9:30am            RNA-Seq Pipeline – Tom Brettin

  • Uploading RNA-seq data
  • Selecting genomes and mapping
  • Downloading and using data in PATRIC
  • RNA Seq Analysis

10:30am          PATRIC and differential expressionMaulik Shukla

11:15am          Exploring Genes Identified by RNA-Seq and transcriptomic analysis – Maulik Shukla

12:00pm          *Lunch*

1:00pm            Comparative Genomics: Protein Families and PathwaysMaulik Shukla

  • Selecting sets of genomes for a study
  • Comparing by region, genes, proteins
  • Comparing pathways
  • Visualizing with heatmap viewer and downloads
  • Acinetobacter use case

3:00 pm           *Day 2: Adjourn*

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