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Title: GTEx exon-exon-junction-level expression summary for Snaptron      
aggregation:
composite digital object
privacy:
not applicable
refinement:
uncurated
ID:
10.5281/zenodo.2577429
storedIn:
Zenodo
availability:
Available
creators:
Benjamin Langmead
Christopher Wilks
keywords:
gtex, rna-seq, splicing
dateReleased:
02-25-2019
description:
GTEx exon-exon-junction-level expression summary from the Snaptron collection. Format is a tab-separated text file compressed and indexed using BGZip, along with supplementary files containing a Tabix index for the data (ending in tbi) as well as two files describing the samples represented in the columns of the data file (ending in tsv). Uses Rail-RNA for spliced alignment. More information at http://snaptron.cs.jhu.edu.
types:
Gene Expression
authors:
Christopher Wilks, Phani Gaddipati, Abhinav Nellore, Ben Langmead
publicationVenue:
Bioinformatics
description:
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. 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.
ID:
10.1093/bioinformatics/btx547
acknowledges:
R01GM118568
title:
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples
dateReleased:
01-01-2018
name:
Messenger RNA level
description:
RNA sequencing reads from the GTEx project
name:
GTEx project
identifier:
R01GM118568
funders:
NIH/NIGMS
description:
CW, AN and BL were supported by NIH/NIGMS grant 1R01GM118568 to BL.
count:
4
title:
GTEx exon-exon-junction-level expression summary for Snaptron
storedIn:
Zenodo
size:
7500
unit:
MB
ID:
SCR:016270
name:
CEDAR Workbench
abbreviation:
CEDAR
homePage: https://cedar.metadatacenter.org

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