Human splicing diversity across the Sequence Read Archive [article]

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
2016 bioRxiv   pre-print
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
more » ... mples 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.
doi:10.1101/038224 fatcat:35kgasp4ebev3pfbndnpi3aoaa