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:
- Basics of working in a terminal
- How to run programs in command line
- How to write bash scripts to run programs in linux/cluster
- From BAM to fastq.gz
- Align fastq.gz files to the genome with STAR
- Quantify genes with STAR –quantmode and HTSeq
- Go from raw counts to normalized expression values
- Basics of R programing
- Quality control steps i.e. sample distance clustering, PCA plots
- Look at differentially expressed genes using models
- Basics of data visualization i.e. heatmaps,boxplots, etc
- 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/
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