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Data Carpentry Genomics Workshop - George Washington University
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1.
Data Carpentry Genomics Workshop - George Washington University
2. Workshop Code of Conduct
2.1. Need Help?
2.2. The Quick Version
2.3. The Less Quick Version
3. Accessing The Atmosphere Cloud
4. Login & Launch Instance
5. SSH Secure-Login
6. Instance Maintenance
6.1. Atmosphere Dashboard
6.2. Suspend Instance
6.3. Delete Instance
7. Additional Features
7.1. Did you know you can access a shell terminal and a web-desktop via your browser ???
8. Advanced Topics
8.1. Atmosphere Advanced Topics
9. Introducing the Shell
9.1. What is a shell and why should I care?
9.2. Navigating your file system
9.3. Summary
9.4. Moving around the file system
9.5. Examining the contents of other directories
9.6. Solution
9.7. Full vs. Relative Paths
10. Bash lesson 2
10.1. Working with Files
10.2. Command History
10.3. Examining Files
10.4. Details on the FASTQ format
10.5. Creating, moving, copying, and removing
10.6. Searching files
10.7. Redirecting output
10.8. File manipulation and more practice with pipes
10.9. Exercise
10.10. Solution
10.11. Writing for loops
11. Working with Bioconda.
11.1. What is bioconda?
11.2. What problems does conda (and therefore bioconda) solve?
11.3. Installing conda and enabling bioconda
11.4. Using conda
11.5. Using bioconda
11.6. Rstudio - Getting started
12. Workflow_Overview
13. Bioinformatics workflows
14. Assessing Read Quality
15. Starting with Data
16. Quality Control
16.1. Details on the FASTQ format
16.2. Assessing Quality using FastQC
16.3. Running FastQC
16.4. Viewing the FastQC results
16.5. Decoding the other FastQC outputs
17. Trimming and Filtering
18. Cleaning Reads
18.1. Trimmomatic Options
18.2. Running Trimmomatic
19. Variant Calling Workflow
20. Alignment to a reference genome
21. Setting up
21.1. Index the reference genome
21.2. Align reads to reference genome
21.3. Sort BAM file by coordinates
21.4. Variant calling
21.5. Explore the VCF format:
21.6. Assess the alignment (visualization) - optional step
21.7. Other Notes
22. Automating a Variant Calling Workflow
22.1. What is a shell script?
23. Analyzing Quality with FastQC
24. Automating the Rest of our Variant Calling Workflow
25. Snakemake Basic Tutorial
26. Open Rstudio
27. Getting started - your first Snakefile
27.1. Updating the Snakefile to track inputs and outputs
27.2. Forcibly re-running things
28. Multiple rules
29. A first refactoring: adding a better default rule
30. A second refactoring: doing a bit of templating
31. Refactoring 3: templating output files, too
31.1. Adding some more files
31.2. Rerunning snakemake
32. Building out the workflow
32.1. Providing input files explicitly to the multiqc rule
32.2. Refactoring this to make it slightly more concise –
32.3. Digression: what files does snakemake check in order to decide about rerunning?
32.4. Making a
clean
rule
32.5. Digression: running things in parallel
32.6. Doing more things in our workflow.
33. More advanced snakemake
33.1. Dry run
33.2. Running things in parallel, revisited
33.3. Specifying software required for a rule
33.4. Outputting the entire workflow diagram
33.5. Snakemake Report
34. Final thoughts - writing your own snakefile
34.1. Dealing with complexity
35. Thinking about workflows - a strong(er) argument
36. Go forth and Workflow!
37. Advanced Topics
38. Transferring Data to and from an Instance
38.1. Transferring Data using iCommands
39. Creating custom Atmosphere Images
40. ssh-rsa-key for password-less login
41. Tmux & Screen
42. SSH Remote host ID Changed Error
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