exon-exon database from RNA-Seq

Question

[mdfardin374]

Hello, Does anyone know how to make the exon-exon junction database assembled from RNA-Seq

[Benn]

This kind of information can be found in annotation databases, for example ensembl. In the GTF files, you can find genomic coordinates of all exons (so also where one exons ends and the next one begins).

Answer 1

[Pierre Lindenbaum]

intropolis is a list of exon-exon junctions found across 21,504 human RNA-seq samples on the Sequence Read Archive (SRA) from spliced read alignment to hg19 with Rail-RNA.

https://github.com/nellore/intropolis