GCRC Bioinformatics Workshops

Hi everyone, on this webpage you will be able to find the links to the sample code, suggested readings, and other resources for the upcoming GCRC Bioinformatics Workshops.

Session 1: From experimental design to data interpretation

Session 2: Aligning your reads to the genome: from FastQ files to raw counts

Session 3: From raw counts to differentially expressed genes

Session 4: Pathway analysis and signatures

Learning Objectives:

  1. Basics of working in a terminal
  2. How to run programs in command line
  3. How to write bash scripts to run programs in linux/cluster
  4. From BAM to fastq.gz
  5. Align fastq.gz files to the genome with STAR
  6. Quantify genes with STAR –quantmode and HTSeq
  7. Go from raw counts to normalized expression values
  8. Basics of R programing
  9. Quality control steps i.e. sample distance clustering, PCA plots
  10. Look at differentially expressed genes using models
  11. Basics of data visualization i.e. heatmaps,boxplots, etc
  12. Basic pathway analysis with the clusterprofiler package

In addition to this webpage, I suggest you check out the blog section of this website for other useful R code and programming tips to help you work through your own data. If you have any additional questions or comments don’t hesitate to contact me.

Other Resources:

Unix/Linux Tutorial for beginners: http://www.ee.surrey.ac.uk/Teaching/Unix/