Research area: genomics

Human splicing diversity across the Sequence Read Archive

Created on 29th January 2016

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;

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 We discuss an application of this resource to cancer involving a recently validated isoform of the ALK gene.

Show more