/
2014 OSU Workshop

2014 OSU Workshop

Jul 30, 2014

Organizers:

Peter R. Hoyt, Dana Brunson

Local Points of Contact:

Peter R. Hoyt, Dana Brunson

Instructors:

  • Peter Hoyt, Dana Brunson (OSU)
  • Haibao Tang, Vivek Krishnakumar (JCVI)
  • Eric Lyons (UA/iPlant)
  • Joshua Orvis
  • Brian Couger

Dates:

August 4-8, 2014

Location:

Bennett Hall Computer Lab, OSU, Stilwater OK

Resources:

Workshop Resources Page

Goal

To provide an interactive, hands-on training on bioinformatics tools and cyberinfrastructure needed to explore entangled genomes.

Pre-Workshop Homework

1. Please test your iPlant credentials to ensure you have access. You can log-in from user.iplantcollaborative.org, click the button "iPlant Login"

  • Once authenticated, click the "My Services" link
  • Under "My Services" please ensure you have access to: Atmosphere and the Discovery Environment. Enter "RNASeq" when prompted for a justification for your Atmosphere allocation. You can also request access to other services at this link
  • If you have account problems, please email support@iplantcollaborative.org

2. Please check your email and this wiki prior to the workshop, as this is the way we will communicate any important changes.

3. Windows users, make sure you have Java installed (http://java.com/en/download/installed.jsp)

Workshop Overview

Here is an overview of the workshop instructors, sponsors, participants and schedule.  Please do not print; you'll receive a hard copy on Monday morning (8 am!)

Daily Schedules

Day

Themes

Instructors

Monday

  • Getting around in Linux/Unix
  • OSU Cowboy
  • File formats (FASTA/FASTQ, GFF/BED, SAM/BAM)
  • RNA-Seq transcript assembly (de-novo and genome guided)
  • Genome Browsing and Visualization

Vivek Krishnakumar
Dana Brunson

Tuesday

  • Genome assembly
  • Genome mapping and variants

Haibao Tang

Wednesday

  • iPlant Discovery Environment
  • iPlant · Atmosphere: An Open Science Cloud
  • Metagenomics with MEGAN
  • Comparative Genomics (CoGe)

Eric Lyons
Peter Hoyt

Thursday

  • Annotation General
  • Annotation (Trinotate?)
  • Metagenomic analyses (microbiome)

Joshua Orvis
Brian Couger

Friday

  • Long-read-NGS data, combining short-read+long
  • Student presentations on assembly and metagenomics

Peter Hoyt

Workshop Notes

Here are a few important links that you may wish to refer to during and after the workshop:

Account/Password Problems

iPlant Help and Discussion Forums

General iPlant Support Issues

iPlant Privacy (And other) policies - "Your Data are Your Data"