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Human splicing diversity across the Sequence Read Archive

By Abhinav Nellore, Andrew E. Jaffe, Jean-Philippe Fortin, José Alquicira-Hernández, Leonardo Collado-Torres, Siruo Wang, Robert A. Phillips, Nishika Karbhari, Kasper D. Hansen, Ben Langmead, Jeffrey T Leek

Posted 29 Jan 2016
bioRxiv DOI: 10.1101/038224 (published DOI: 10.1186/s13059-016-1118-6)

We aligned 21,504 publicly available Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon junctions with junctions in several recent gene annotations. 56,865 junctions (18.6%) found in at least 1,000 samples were not annotated, and their expression associated with tissue type. Newer samples contributed few novel well-supported junctions, with 96.1% of junctions detected in at least 20 reads across samples present in samples before 2013. Junction data is compiled into a resource called intropolis available at http://intropolis.rail.bio. We discuss an application of this resource to cancer involving a recently validated isoform of the ALK gene.

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