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

Class Notes

• Introduction to iPlant Atmosphere
• Introduction to Terminal
  • Overview of Linux
    • Linux System Structure
  • Starting a Shell
  • Terminal Commands
    • pwd (Print Working Directory)
    • mkdir (makding a directory)
    • ls (list)
    • cd (change directory)
    • Excercise
  • File Handling Through the Terminal
    • Displaying Content of a Compressed gunzip File
    • De-compressing gunzip File
    • Displaying Content of a File
    • Renaming a File
    • Searching the Contents of a File
    • Concatenating two or more files
    • Finally, Compress that File!!
    • Excercise
• How to Install Software on Linux
  • Software we need
    • Quality Control
    • Alignment Software
  • Ways to Install Software
    • 1. Install Software From Your Distribution’s Repositories
    • 2. Downloading and Unpacking a Binary Archive
    • 3. Compileing From Source
• Data Analysis in the Terminal
  • Quality Control
    • Quaulity Check With Fastqc
    • Adapter Trimming with scythe
    • Quality Trimming with sickle
  • Short-reads Alignment with Tophat2
    • Indexing your Genome
    • Aligning Short Reads
  • Excercise

Indices and tables

• Index
• Module Index
• Search Page