Fall DE Workshop

November 11, 2019 – November 15, 2019 all-day
National Center for Genome Resources
2935 Rodeo Park Dr. E
Ethan Price

NCGR Fall 2019 Bioinformatics workshop on Differential gene Expression (DE)



The National Center for Genome Resources (NCGR), Santa Fe, NM


November 11 – 15, 2019 (5 days)


This program is geared towards training biologists (undergraduates, graduates and researchers) with minimal or no bioinformatics experience. Space is limited.


Students will acquire the skill-set to independently analyze RNA-Seq data using the command line interface, analytical workflows and current DE tools. UNIX fundamentals, RNA-Seq, data QC, alignments, read count generation, featureCounts, DE and pathway analysis will be taught.

Topic overview

DE entails examining the fraction of the genome that is responsible for making products that drive organismal function. Gene expression is influenced by various extrinsic physiological and environmental as well as several intrinsic properties of the organism. Whole transcriptome profiles are becoming increasingly popular, useful and generate large volumes of data. Knowing how to handle, analyze, and make biological inferences on this scale of data is a valuable skill-set for students and researchers.

Workshop Rates

New Mexico Students & New Mexico Academic Researchers Free
All other students $1,500
IDeA Researchers $1,750
Academic, Military, Government $2,250
Commercial $2,750

Lodging scholarships (for NM students only)

If you are not a NM student, check to see if you are from an INBRE funded state, here. If so, connect with your local INBRE Administrative Core to see if funding is available to support your educational pursuit to attend our workshop.

Application Form Fill out this online application here: Bioinformatics Training Application

Application Due 11:59pm September 30th, 2019 (MST)   Late applications will not be accepted.  Selection Committee to select interns shortly after the deadline. If any questions arise while reviewing your application packet, we will contact you directly.

Unix Prerequisites

  1. Beginner’s guide to the Bash terminal: https://www.youtube.com/watch?v=oxuRxtrO2Ag
  2. Review Introduction to the UNIX Operating System and Tutorials 1 – 4 at: http://www.ee.surrey.ac.uk/Teaching/Unix/
  3. and also Review vi editor: https://www.cs.colostate.edu/helpdocs/vi.html 

What to expect upon acceptance

1)    Email confirming acceptance into the internship program, and further details.
2)    Dataset (if applicable) to be sent to Project Coordinator, Ethan Price by October 21st, 2019


Travel to and from Santa Fe, NM.   The Santa Fe Regional Airport is approximately 7 miles away (15-minute drive to the hotel) and Albuquerque International Sunport is approximately 60 miles away (1-hour drive to the hotel).   Santa Fe airport is very convenient.

Public city transportation.   Available if needed. There is a city bus stop 400 ft from NCGR and the Zia train station approximately ¼ mile from Santa Fe Suites.  These can be used to visit downtown Santa Fe, sightseeing or other destinations.

Lodging Information and Food

Santa Fe Suites.  Lodging will be provided at the student rate of $50 per night ($300.00 for 6 nights plus tax) for a single queen room.   Santa Fe Suites is approximately ½ mile away and a 15-minute walk to NCGR.  NCGR staff can always lend a hand with transportation to and from Santa Fe Suites if needed (e.g. inclement weather) as well.

Food. Just around the corner from the Santa Fe Suites is an Albertson’s supermarket where students may purchase groceries.  Also, there are a number of restaurants in the area (sandwiches, Chinese food, pizza, etc.).  The hotel serves a free continental breakfast each morning and we may occasionally organize lunch outings at local Santa Fe eateries as a group (optional).  Santa Fe has excellent food—we are known for our green and red chiles!  We estimate total food expenses for the week to be $70 – $150.


Please contact Project Coordinator, Ethan Price, with any additional questions you may have at eprice@ncgr.org and we look forward to your participation!

Sponsored by New Mexico IDeA Network for Biomedical Research Excellence (NM-INBRE).


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