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1. Welcome to SETAC-NA 2018 RNAseq workshop!
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Table of contents
¶
1. Welcome to SETAC-NA 2018 RNAseq workshop!
1.1. Instructors
1.2. Schedule in brief
1.3. Other info
2. Workshop Code of Conduct
2.1. Need Help?
2.2. The Quick Version
2.3. The Less Quick Version
3. Introductions
3.1. Here are your instructors for the day:
4. Booting a Jetstream Computer Instance for your use!
4.1. Resources
4.2. Request to log in to the Jetstream Portal
4.3. Use “XSEDE”
4.4. Fill in the username and password and click “Sign in”
4.5. Select Projects and “Create New Project”
4.6. Name the project for yourself, click “create”
4.7. Boot an instance with a pre-built image
4.8. Find the “RNASeq_1DayWorkshop” base image (Oct 15, 2018 by ljcohen), click on it
4.9. Name it something simple
4.10. Wait for it to become active
4.11. Click on your new instance to get more information!
4.12. Miscellany
4.13. Suspend your instance
4.14. Shutting down your instance
4.15. Deleting your instance
5. Logging in to jetstream from your local terminal with a key file
5.1. Concerning Keys
5.2. Getting the Private Key
5.3. Getting your instance IP address
5.4. On MacOS/Linux
5.5. On Windows
6. Jetstream: working with bioconda.
6.1. What is bioconda?
6.2. What problems does conda (and therefore bioconda) solve?
6.3. Installing conda and enabling bioconda
6.4. Using conda
6.5. Using bioconda
6.6. Rstudio - Getting started
7. Using the command line
7.1. Goals
7.2. Background
7.3. What does it look like?
7.4. Usage
7.5. Navigating Files and Directories
7.6. Creating files and folders
7.7. Piping
7.8. Grep, tr, wc, mv and many others
8. Short read quality and trimming
8.1. Data source
8.2. Check that your data is where it should be
8.3. Quality trimming and light quality filtering
9. De novo transcriptome assembly
9.1. Link in the trimmed data
9.2. Run the assembler
9.3. Looking at the assembly
9.4. Suggestions for next steps
10. Read Quantification
10.1. Make a new working directory and link the trimmed reads and assembly
10.2. Index the assembly:
10.3. Run salmon on all the samples:
10.4. Take a look at quant output
10.5. Look at all the mapping rates:
10.6. More reading
11. Differential expression analysis with DESeq2
11.1. RUN THIS DURING LUNCH BREAK
11.2. Move salmon output quant files to their own directory
11.3. Copy a previously-made gene and transcript id relationship file to your home directory
11.4. Grab a special script plotPCAWithSampleNames.R
11.5. Rstudio reminder
11.6. Working in Rstudio:
12. Backup files
12.1. Input raw fastq data
12.2. Trimmed reads
12.3. Transcriptome assembly
12.4. Annotation, created with this annotation lesson
12.5. Salmon quantification files
13. Instructions for creating a Jetstream image
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