Related Experiment Video
Updated: Feb 3, 2026

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
Published on: June 8, 2020
Building Portable and Reproducible Cancer Informatics Workflows: An RNA Sequencing Case Study
Gaurav Kaushik1, Brandi Davis-Dusenbery2
1Foundation Medicine, Cambridge, MA, USA.
Abstract:
The Seven Bridges Cancer Genomics Cloud (CGC) is part of the National Cancer Institute Cloud Resource project, which was created to explore the paradigm of co-locating massive datasets with the computational resources to analyze them. The CGC was designed to allow researchers to easily find the data they need and analyze it with robust applications in a scalable and reproducible fashion. To enable this, individual tools are packaged within Docker containers and described by the Common Workflow Language (CWL), an emerging standard for enabling reproducible data analysis. On the CGC, researchers can deploy individual tools and customize massive workflows by chaining together tools. Here, we discuss a case study in which RNA sequencing data is analyzed with different methods and compared on the Seven Bridges CGC. We highlight best practices for designing command line tools, Docker containers, and CWL descriptions to enable massively parallelized and reproducible biomedical computation with cloud resources.
Related Concept Videos
Eukaryotic RNA Polymerases
All three eukaryotic RNAPs require specific transcription factors, of which the...
RNA Editing
RNA Interference
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
RNA Splicing
RNA Stability
Bacterial RNA Polymerase
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...

