Education - Transcriptome Analysis Workshop

Transcriptome Analysis Workshop

This workshop will provide a detailed introduction to transcriptome sequencing and informatics concepts. It will provide training on analyses of RNA-Seq data including the use of different analytical tools, relevant file formats, reference genomes, transcriptome annotations, quality control measures, reference-based alignment, gene expression, and differential gene and isoform analyses. These tutorials will be accompanied by hands-on exercises using complete analytical pipelines on test datasets.

Included topics

  • Transcriptome sequencing techniques
  • QC considerations
  • Read alignment with Bowtie, and HISat
  • Expression quantification using HTSeq
  • Differential expression with DEseq
  • Isoform analysis with Cufflinks
  • Differential Isoform analysis with CuffDiff
  • Pathway Analysis with IPA, GOrilla, and DAVID
  • Primer on single-cell RNASeq

Dates and Registration

The registration fee for this workshop is $450 for general rate, $250 for student rate.

Postponed to Sept. 15-17, 2020


Location and Times

The course will be held on the University of Maryland Baltimore campus in the Health Sciences Facility, Building 3, at 670 W. Baltimore St., Baltimore, MD 21201 [Google map].

These workshops are 2.5 days long. They will begin in the afternoon of the first day with registration/check-in from 12:30 to 1:00. The workshop will run from 1:00-5:00 the first day and from 9:00-5:00 the remaining two days. Breakfast (continental) and lunch will be provided on the second and third days (the two full days).

Driving Directions

Directions can be found here. There are two parking garages that you could use. One is the Saratoga garage located at 220 Arch St. The other is the BioPark garage located at 1 N. Poppleton St. Cost is $12 per day. There is also street parking that might be closer. Pay for this at pay stations along the streets. There is usually a 2 or 4 hour limit on how long you can be there without paying again.


The closest airport is Baltimore Washington International Thurgood Marshall Airport (BWI). Other airports in the region (1 - 1.5 hours away) are Dulles and Reagan National.


Baltimore is served by Amtrak and MARC train service.


There are several hotels within easy walking distance to our location at 670 W. Baltimore St. Here are a couple of suggestions that previous attendees have been happy with:

Hampton Inn Baltimore-Downtown-Convention Center
Holiday Inn Baltimore-Inner Harbor (Downtown)


Please send any questions to Michelle Giglio (mgiglio AT