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 - BKJ_projectsetup
  2. Quality control and trimming of short RNA-seq reads - BKJ_qctrim
  3. Workflows for reference-based and reference-free transcriptome analysis - BKJ_aligncount and BKJ_refvsnoref
  4. Differential gene expression and some potential pitfalls - BKJ_diffexp

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 log back onto your EC2 instances that you were using yesterday. If you have forgotten how to log on, head back to the main page and follow the instructions from yesterday.

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

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.