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Workshop Code of Conduct
The Quick Version
The Less Quick Version
SIO Nonmodel mRNASeq Workshop (2017)
Workshop materials
Booting a Jetstream Computer Instance for your use!
Request to log in to the Jetstream Portal
Use “XSEDE”
Fill in your username and password and click “Sign in”
Select Projects and “Create New Project”
Name the project and click “create”
Select the newly created project
Within the project, select “new”
Find the “Ubuntu 16.04” image, click on it
Name it something simple and select ‘m1.medium’
Wait for it to become active
Click on your new instance to get more information!
Miscellany
Suspend your instance
Shutting down your instance
Deleting your instance
Short read quality and trimming
Installing some software
Data source
Check that your data is where it should be
Quality trimming and light quality filtering
De novo transcriptome assembly with Trinity
Installation
Then, let’s check we still have our reads from the QC lesson
Running the Assembly!
Evaluating your transcriptome assembly
Install
Transrate
BUSCO
Analyzing RNAseq expression with Salmon
Getting Started
Installation
Download and make Salmon available in the path
Then, let’s check we still have our reads from yesterday’s QC work
Download or link an assembly
Run Salmon
Working with the counts
Other useful tutorials and references
Differential expression analysis with DESeq2
Upgrade R (3.4.x)
Install RStudio Web server
Make sure you’re running RStudio
Install DESeq2 prereqs
Move salmon output quant files to their own directory
Download gene and transcript id relationships to your home directory
Grab a special script plotPCAWithSampleNames.R
RStudio!
Annotating de novo transcriptomes with dammit
Installation
Database Preparation
Annotation
Parse dammit output
References
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