2015 OSU Workshop: Wednesday

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Lecture: de novo RNA-Seq (8:30 - 9:30)

1. RNA-seq Reference-based and Genome-guided Assembly (Lecture): http://goo.gl/lIQ2oW

Hands on exercises: (9:30 - 2:00PM)

1. Transcriptome analysis using Arabidopsis as a reference genome: https://pods.iplantcollaborative.org/wiki/x/jKai
2. Transcriptome analysis without an available reference genome: https://pods.iplantcollaborative.org/wiki/x/RY3e

Lecture: Introduction to iPlant -- Peter Hoyt (1:00-2:00PM)

Slides: https://drive.google.com/open?id=0BwLI3KMs2RkrQk5KVUlYMUlSM0E

• Lecture – The iPlant Discovery Environment and Data Store
  • Login and Directory structure
  • Opening and using Apps
  • Saving and Managing Data

(2:00PM - 3:30PM)

Hands on exercises: https://drive.google.com/open?id=1b-l0Be4pBEm4FS3kuJ34PWu35js6bW3uBU5OuqU-O8o

• Signing Into The Discovery Environment and Simple Uploads
• Using Apps in the Discovery Environment
• Installing and Using iDROP http://de.iplantcollaborative.org/dl/d/BB298AD6-3E1C-4004-A1B3-82705AD1D2C3/iDrop_windows-x64_2_0_1-beta3.exe
• Performing Quality Control on Sequence Data
• (Optional) Fixing datafiles
• (Optional) BlastX of clean data on Cowboy

NEXT:

Catch-up time for Exercises as needed

OR:

The iPlant Atmosphere

Lecture: The iPlant Atmosphere -- Peter Hoyt  (3:30 - 5:00)

Slides:  https://drive.google.com/open?id=0BwLI3KMs2RkrdVRpN0xIYnpYU3M

• About Instances
• Creating NEW Instances
• Mounting a volume and creating a file system
• Accessing your Instance
  • Using Shell
  • Using VNC
  • Using Putty
• Restoring data from the Data Store
• iCommands

Hands on exercise: https://drive.google.com/open?id=0BwLI3KMs2RkrTmkwN2J4dFp3clE

• Starting a new instance (Use 5 groups)
• Creating a new volume
• Attaching, mounting and putting filesystem on new volume
• Connecting to your Atmosphere Instance
  • Shell
  • Putty
  • VNC on Chrome
• Using iCommands
  • for complete instructions read: https://wiki.irods.org/index.php/icommands
• Creating folders and files with VNC
• Sharing your VNC Shession

Wrap-up (5:00- )