Module 1
Week 1 Introductions and File systems
L1 Why bioinformatics?
L2 Intro to statistics?
Lesson 1
- Intro to Course, learning objectives
- Intro to Unix
- operating system
- What is a shell (how to proceed Windows vs Mac)
- What is conda?
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Getting started with DNAnexus
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Help Session: DNAnexus trouble shooting
Lesson 2: Understanding and navigating file systems
- Navigating file systems
- Best practices in file organization and naming conventions
- Using unix (12 commands and more)
Week 2
Lesson 3 Intro to Biowulf
- What is Biowulf? Explaining compute nodes, cores, CPUs, and the idea of connecting to a remote system
- Why work on Biowulf?
- Available software, increased computation power, high memory jobs, big data
- Connect to Biowulf
- Explain Biowulf file systems (home, data, lscratch)
- Biowulf module system
- Safeguards, getting help
- Help Session:
Lesson 4: Working on Biowulf
- Slurm system: batch jobs, swarms jobs, interactive sessions
- Introduce parallel command
- Retrieve data from NCBI
- Trouble shooting jobs and job failures
- Help session: submitting jobs on Biowulf
Week 3
Lesson 5 Review and Downloading and organizing files for RNASeq files
- Review (30 min)
- file compression and data set introduction (30 min)
-
setting up project folders
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Help session: Coding scavenger hunt?
Lesson 6 Pattern searching with grep and egrep
Week 4
Lesson 7 Sequencing Facilities and data types (Des)
Lesson 8 RNA-Seq from Experimental design to analysis (Peter)
Notes: linux - how to get help (man, flags) file permissions - changing permissions include grep and regular expressions