The BaseSpace® RNA-Seq Alignment v1.0 App supports RNA sequencing read alignments, variants calling, gene fusions detection, and novel script assembly with Cufflinks. The app can run STAR and tools from the Tuxedo Suite (Bowtie, TopHat, Cufflinks) to produce aligned reads, variant calls, and FPKM abundance estimates of reference genes and transcripts. Also, the app can perform fusion calling using Manta-fusion or TopHat-fusion tools.

The Cufflinks Assembly & DE v2.0 App uses the analysis results from the RNA-Seq Alignment App to perform novel transcript merging and differential expression.