Rail-RNA

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive
We found 56,861 junctions (18.6%) in at least 1000 samples that were not annotated out of 21,504 samples, and their expression associated with tissue type. We compiled junction data into a resource called intropolis available at http://intropolis.rail.bio.
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Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive
Rail-RNA: Scalable analysis of RNA-seq splicing and coverage
We describe Rail-RNA, a cloud-enabled spliced aligner that analyzes many samples at once. Rail-RNA eliminates redundant work across samples, making it more efficient as samples are added. For many samples, Rail-RNA is more accurate than annotation-assisted aligners.
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Rail-RNA: Scalable analysis of RNA-seq splicing and coverage