Dataset Information
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples.
Ontology highlight
ABSTRACT: Motivation
As more and larger genomics studies appear, there is a growing need for comprehensive and queryable cross-study summaries. These enable researchers to leverage vast datasets that would otherwise be difficult to obtain.Results
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 score junctions according to tissue specificity or other criteria, and can score samples according to the relative frequency of different splicing patterns. We describe the software and outline biological questions that can be explored with Snaptron queries.Availability and implementation
Documentation is at http://snaptron.cs.jhu.edu. Source code is at https://github.com/ChristopherWilks/snaptron and https://github.com/ChristopherWilks/snaptron-experiments with a CC BY-NC 4.0 license.Contact
chris.wilks@jhu.edu or langmea@cs.jhu.edu.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Wilks C
PROVIDER: S-EPMC5870547 | biostudies-literature | 2018 Jan
REPOSITORIES: biostudies-literature
Publications
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples.
Bioinformatics (Oxford, England) 20180101 1
<h4>Motivation</h4>As more and larger genomics studies appear, there is a growing need for comprehensive and queryable cross-study summaries. These enable researchers to leverage vast datasets that would otherwise be difficult to obtain.<h4>Results</h4>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-se ...[more]