Process of Analyzing eQTL Data

So far,

1. Overview of Next Generation Sequencing
2. Setting an iPlant account
3. Uploading data to iPlant
4. Intrdouction to iPlant Discovery Environment
5. QC and cleaning sequence data
6. Mapping of reads to the genome
7. Assembling transcripts and estimating their abundances

Today,

1. Introduction to iPlant Atmosphere
2. Introduction to Terminal
3. Doing down stream analysis in the Terminal

Contents

• iPlant Atmosphere: Introduction Introduction to iPlant Atmosphere, this includes:

  • What is iPlant Atmosphere ?
  • Requesting Access to Atmosphere
  • Logging In to and Signing Out of Atmosphere
  • Using Instances
    • Launching a New Instance
    • Logging in to an Instance
    • Rebooting, Stopping and restarting an instance, and Suspending an instance

• Introduction to Terminal: Here you will learn basic terminal commands, how to transfer your data to cloud service and install software in Linux

  • Data Transfer
  • File Handling
  • Install Software

• Doing down stream analysis in the Terminal Run fastqc, sickle,scythe, tophaht2 in commandline