Transcriptome Assembly  
March 22 and 29 2017

This workshop will cover practical issues related to transcriptome assembly from RNA-Seq reads using Trinity software (  from Broad Institute on BioHPC lab machines. The first session will cover RNA-Seq read preparation, setting up, monitoring, and restarting a Trinity run, memory and CPU requirements for typical Trinity jobs. In the second session, we will discuss differential expression analysis using Trinity transcriptomes. All topics will be illustrated with hands-on exercises performed by participants at their own pace on the assigned BioHPC Lab computers, during the workshop or at home, using the provided step-by-step instructions. 

Please note: Transcriptome annotation issues will be covered in a different workshops (Gene Function Annotation).

Workshop attendees are encouraged to bring laptop computers to serve as terminals to the Bioinformatics Facility's BioHPC Lab workstations where the actual computations will take place. Our workstations run Linux operating system, so if you are new to Linux computing environment you may want to attend our free  workshops "Introduction to BioHPC Lab" and "Linux for Biologists". You can also use both workshop materials posted online to refresh your Linux skills:

Linux for Biologists Part 1   Linux for Biologists Part 2  Linux for Biologists Part 3

The registration fee is $100. Bioinformatics Facility is organizing 6 workshops in the Spring 2017 - if you'd like to register for all of them at a reduced rate please go to this page.

Access to BioHPC Lab workstations requires a Lab account. If you do not yet have an account on BioHPC Lab system, we will create one for you. Also, we will assign a machine for you to work on during and after the workshop.

The machine allocations are posted here.

Workshop Outline
Session 1 3/22/2017 3:30:00 PM 655 Rhodes Hall
Session 2 3/29/2017 3:30:00 PM 655 Rhodes Hall
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