RT Journal Article
SR Electronic
T1 MAJIQ-SPEL: Web-Tool to interrogate classical and complex splicing variations from RNA-Seq data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 136077
DO 10.1101/136077
A1 Christopher J. Green
A1 Matthew R. Gazzara
A1 Yoseph Barash
YR 2017
UL http://biorxiv.org/content/early/2017/05/09/136077.abstract
AB Analysis of RNA sequencing (RNA-Seq) data have highlighted the fact that most genes undergo alternative splicing (AS) and that these patterns are tightly regulated. Many of these events are complex, resulting in numerous possible isoforms that quickly become difficult to visualize, interpret, and experimentally validate. To address these challenges, We developed MAJIQ-SPEL, a web-tool that takes as input local splicing variations (LSVs) quantified from RNA-Seq data and provides users with visualization and quantification of gene isoforms associated with those. Importantly, MAJIQ-SPEL is able to handle both classical (binary) and complex (non-binary) splicing variations. Using a matching primer design algorithm it also suggests users possible primers for experimental validation by RT-PCR and displays those, along with the matching protein domains affected by the LSV, on UCSC Genome Browser for further downstream analysis.Availability: Program and code will be available at http://majiq.biociphers.org/majiq-spel