Tuesday 24th Nov
| Time |
What |
| 09:30 |
Speaker |
| 10:00 |
DNA variant calling |
| 10:45 |
Break |
| 11:00 |
DNA variant calling cont. |
| 12:15 |
Lunch |
| 13:00 |
DNA variant calling cont. |
| 14:30 |
Break |
| 14:45 |
DNA variant calling cont |
| 16:30 |
End of Day |
Background
Learning objectives:
- Why study E. coli?
- Understand the data set.
- What is hypermutability?
Lesson:
Data Carpentry - Genomics: Background and Metadata
Assessing Read Quality
Learning objectives:
- Explain how a FASTQ file encodes per-base quality scores.
- Interpret a FastQC plot summarising per-base quality across all reads.
- Use
for loops to automate operations on multiple files.
Lesson:
Data Carpentry - Genomics: Assessing Read Quality
Trimming and Filtering
Learning objectives
- Clean FASTQ reads using Trimmomatic.
- Select and set multiple options for command line bioinformatic tools
- Write
for loops with two variables.
Lesson:
Data Carpentry - Genomics: Trimming and Filtering
Variant Calling Workflow
Learning objectives:
- Understand the steps involved in variant calling.
- Describe the types of data formats encountered during variant calling.
- Use command line tools to perform variant calling.
Data Carpentry - Genomics: Variant Calling Workflow
Automating a Variant Calling Workflow
Learning objectives
- Write a shell script with multiple variables.
- Incorporate a
for loop into a shell script.
Introduction to Version Control (Git)
Learning objectives
- Understand the benefits of an automated version control system.
- Understand the basics of how automated version control systems work.
- Configure
git the first time it is used on a computer.
- Understand the meaning of the
--global configuration flag.
- Create a local Git repository.
- Describe the purpose of the
.git directory.
- Go through the modify-add-commit cycle for one or more files.
- Explain where information is stored at each stage of that cycle.
- Distinguish between descriptive and non-descriptive commit messages.
- Identify and use Git commit numbers.
- Compare various versions of tracked files.
Lessons: