Introduction
The BaseSpace Sequence Hub RNA-Seq Alignment App supports RNA sequencing read alignments, variants calling, and gene fusions detection. The app can run STAR, Strelka, and Salmon. The app uses these tools to produce aligned reads, variant calls, and TPM abundance estimates of reference genes and transcripts. Also, the app can perform fusion calling using Manta-fusion.
The RNA-Seq Differential Expression App uses the analysis results from the RNA-Seq Alignment App to perform differential expression analyses.