Introducing BaseSpace RNA-Seq Core Apps!

The BaseSpace team is excited to announce the release of our most anticipated applications since the announcement of the Native App Engine last October.


  • The TopHat Alignment App can be used to align RNA reads as well as detect gene fusions using the industry-standard method. Illumina’s Isaac method further enables the calling of SNVs and small indels.
  • The Cufflinks Assembly & Differential Expression App enables gene expression profiling and detection of novel transcript isoforms.



These applications are part of the BaseSpace Core Apps and were both written with our Native App Engine, taking advantage of the parallelization features which allows TopHat to process 96 samples in less than a couple hours with fusion calling enabled.  This parallelization is seamless and automatic, bringing the scalability of the cloud to your analysis – so that if you have 1 sample or 100, they run in the same amount of time.

In the coming days, we will be posting a sample project with fully analyzed data so that you can quickly view the output from the RNA-Seq Core Apps.  There is also example data comparing Universal Human Reference and Human Brain mRNA that you can import into your BaseSpace account from BaseSpace’s Public Data repository:


For more information about these apps, check out the detailed announcement here.  If you’d like to try out the new RNA-Seq Apps in BaseSpace, head over to BaseSpace Apps.

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