PATRIC Workshop – San Diego State University¶
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 PATRIC – Bob Olson
Uploading reads and read libraries
Selecting assembly methods for comparison
Queuing jobs and retrieving results
Analyzing assembly output and comparisons
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
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
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
10:30am PATRIC and differential expression – Maulik Shukla
Differential expression
11:15am Exploring Genes Identified by RNA-Seq and transcriptomic analysis – Maulik Shukla
Exploring gene expression in datasets available in PATRIC
Downstream analysis of RNA-Seq genes
Examining the genes identified as significantly expressed by RNA
Looking for data on antibiotic resistance genes
12:00pm *Lunch*
1:00pm Comparative Genomics: Protein Families and Pathways– Maulik Shukla
Selecting sets of genomes for a study
Comparing by region, genes, proteins
Comparing pathways
Visualizing with heatmap viewer and downloads
3:00 pm *Day 2: Adjourn*
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