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Unix Tutorial Part 2: Shell Scripting

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Jeanie Lim edited this page Sep 11, 2016 · 2 revisions

Progress http://swcarpentry.github.io/shell-novice/04-pipefilter/ http://swcarpentry.github.io/shell-novice/06-script/

Shell Scripting

We are finally ready to see what makes the shell such a powerful programming environment. We are going to take the commands we repeat frequently and save them in files so that we can re-run all those operations again later by typing a single command. For historical reasons, a bunch of commands saved in a file is usually called a shell script, but make no mistake: these are actually small programs.

We are going to write a shell script that runs a series of commands for a fixed set of files

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The Unix Shell Bootcamp

#Table of Contents

  1. Module 0 Setting Up for Data Analysis
    1. Introduction to High Performance Computing Cluster
    2. Connecting to MGHPCC
    3. Computing Environment
    4. Unix Tutorial Part 1: UNIX Bootcamp
    5. Unix Tutorial Part 2: Shell Scripting
    6. Unix Tutorial Practice
    7. Submitting computing jobs to HPC using LSF
    8. Ignore: Git Tutorial
  2. Module 1 Introduction/ Overview
    1. Overview of RNA-seq Experiment
    2. RNA-Seq Analysis Pipeline
    3. RNA-Seq Input Data
    4. RNA-seq File Formats and Software-Specific Files
    5. Getting Data for Analysis
  3. Module 2 Quality Control
    1. Data Quality Assessment
    2. Analyzing FastQC Report
    3. Adapter Removal, Trimming, and Filtering
  4. Module 3 Tuxedo Pipeline
    1. The Tuxedo Pipeline
    2. Read Alignment with TopHat2
    3. Transcript Assembly with Cufflinks
    4. Differential Analysis with Cuffdiff
    5. Visualization with CummeRbund
  5. Resources and Reference
    1. Resource: RNA-Seq Analysis Techniques
    2. Resource: Tools for RNA seq Analysis
    3. Resource: Concepts in sample preparation and library construction that can influence study design, analysis and interpretation
    4. Common RNA seq analysis questions and their answers
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