Event box

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


  1. 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. 
  1. A laptop/desktop with MAC OS X, or Linux;      or Windows with Mobaxterm installed (a free version works).
  2. 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)

  1.  copy the link to your project from your sequencing-data-ready email
  2.  prepare a sample info file with two columns (folder name, group name)
  3.  modify a config file by adding the group contrasts desired (an example below)
    - A-Ctrl
    - B-Ctrl
  4. Then paste a one-line command and sit back for one hour or less
  5. 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
Registration has closed.

Event Organizer

Profile photo of Rolando Garcia-Milian
Rolando Garcia-Milian