RNA-seq and Differential Gene Expression in Bacteria

Today we have a few objectives we would like to cover:

  1. Set up a project for your data analysis for reproducible and robust analysis - Setting up your RNA-seq project
  2. Quality control and trimming of short RNA-seq reads - Quality control and trimming of reads
  3. Workflows for reference-based and reference-free transcriptome analysis - Align and count gene features and Considerations for reference vs reference-free transcriptome analysis
  4. Differential gene expression and some potential pitfalls - Differential gene expression

Learning goals

  • Familiarize yourself with creating documentation and data organization strategies
  • Perform and assess read trimming and quality
  • Analyze reference and reference-free transcriptome analysis through available workflows
  • Understand underlying assumptions and potential issues with differential gene expression

At this point, go ahead and start up new m3.xlarge EC2 instances, as you did yesterday (see: Getting started with Amazon EC2).

Additional Resource - Basic Linux/Unix commands

To refresh your memory on some basic Linux/Unix commands, we will cover the basic commands necessary to:

1. Move through folders

2. List the contents of a folder

3. Make new folders

4. Rename files/folders

5. Delete files/folders

  Command What it does... Examples
1. cd Change directory/folder > cd ~ (this changes to your home directory); > cd .. (this goes back one folder)
2. ls List the contents of a folder > ls
3. mkdir Make a new directory/folder > mkdir NewFolder (this will make a new folder called ‘NewFolder’ in your current directory)
4. mv Rename or move a file from one name to another > mv file1 file2 (this will rename/move file1 to file2)
5. rm Remove a file (add the -r flag to remove a folder) > rm file1 (remove file1); > rm -r folder1 (remove folder1)

Command reference sheet

Linux/Unix command list

(Ref. sheet from: http://files.fosswire.com/2007/08/fwunixref.pdf)

Next: Setting up your RNA-seq project

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