BMS5021 Topic 2
1
Welcome to BMS5021 - Introductory Bioinformatics
1.1
Navigating the course manual
1.2
Learning programming
2
The linux command line and HPC
2.1
Working on the command line
2.2
Accessing the BMS5021 command line interface
3
Week 1 Part A - Introduction to the Shell
3.1
Learning Objectives
3.2
Workshop setup
3.3
Navigating on the command line
3.4
Creating files and directories
3.5
Copying, moving and deleting files
3.6
Wild cards
3.7
Viewing file content
3.8
Searching file content
3.9
Editing files - Sed
3.10
Editing files - Nano
4
Week 1 Part B - Introduction shell scripting and pipelines
4.1
Learning Objectives
4.2
Workshop setup
4.3
Redirects and pipes
4.4
Constructing basic FOR loops
4.5
Constructing basic WHILE loops
4.6
Setting variables
5
Week 2 Part A - Quality control in Bioinformatic Sequence Analysis
5.1
Learning Objectives
5.2
Workshop setup
5.3
The impact of gamma radiation on gene expression
5.4
Quality control of sequencing reads
5.5
Trimming reads with TrimGalore!
5.6
Trimming reads with Trimmomatic
6
Week 2 Part B - Quantification with Kallisto
6.0.1
Transcript quantification with Kallisto
7
Week 3 - Comparing bioinformatic pipelines
7.1
Learning Objectives
7.2
Workshop setup
7.3
Assessing the influence of bioinformatic tools on results
7.4
Comparing isoform expression quantification
7.5
Differential gene expression analysis
References
BMS5021 - Introductory Bioinformatics Manual
References