RT Journal Article
SR Electronic
T1 Snaptron: querying and visualizing splicing across tens of thousands of RNA-seq samples
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 097881
DO 10.1101/097881
A1 Christopher Wilks
A1 Phani Gaddipati
A1 Abhinav Nellore
A1 Ben Langmead
YR 2017
UL http://biorxiv.org/content/early/2017/01/09/097881.abstract
AB As more and larger genomics studies appear, there is a growing need for comprehensive and queryable cross-study summaries. Snaptron is a search engine for summarized RNA sequencing data with a query planner that leverages R-tree, B-tree and inverted indexing strategies to rapidly execute queries over 146 million exon-exon splice junctions from over 70,000 human RNA-seq samples. Queries can be tailored by constraining which junctions and samples to consider. Snaptron can also rank and score junctions according to tissue specificity or other criteria. Further, Snaptron can rank and score samples according to the relative frequency of different splicing patterns. We outline biological questions that can be explored with Snaptron queries, including a study of novel exons in annotated genes, of exonization of repetitive element loci, and of a recently discovered alternative transcription start site for the ALK gene. Web app and documentation are at http://snaptron.cs.jhu.edu. Source code is at https://github.com/ChristopherWilks/snaptron under the MIT license.