Introduction to RNA-seq Analysis on the Yale Clusters
- Got the email from west campus or stem cell center titled 'your sequencing data is ready'?
- You can now have your data analyzed on one of the Yale HPC clusters
- all by yourself,
- from mapping to differential expressed genes
- from PCA to volcano plots and heatmaps
- from venndiagrams to geneset enrichment
- all finished within an hour, no matter your have 6 samples or 60
- apply for an account on farnam and/or ruddle: it just takes you ONE minute!
Go to account request page of yale center for research computing
- check farnam, also check ruddle if you have sequenced on west campus/YCGA. Note: it might takes a few work days for your accounts to be approved.
- Don't waste time to log in, once you get the approved email, I can help you log in a minute.
- A laptop/desktop with MAC OS X, or Linux; or Windows with Mobaxterm installed (a free version works).
- Walked through Command-line Bootcamp or other basic linux command tutorials.
A one-line command on the HPC (will be detailed during workshop)
How to use: (will be detailed during workshop)
- copy the link to your project from your sequencing-data-ready email
- prepare a sample info file with two columns (folder name, group name)
- modify a config file by adding the group contrasts desired (an example below)
- Then paste a one-line command and sit back for one hour or less
- Finally, paste a one-line command and download everything from the HPC cluster to your computer.
What to expect during the two-hour workshop:
- We will walk through a case study, from setting up to reporting.
- I will help up to ten qualified attendees (see requirements) get set up and run the example sequencing project on farnam.
- Workflow explained and results interpreted.
I can take follow up email requests from attendees to improve/add functional blocks to the workflow
- Monday, October 30, 2017
- 2:00pm - 4:00pm
- Cushing/Whitney Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520
- Medical School