MAJIQ: Modeling Alternative Junction Inclusion Quantification
MAJIQ and Voila are two software packages that together detect, quantify, and visualize
local splicing variations (LSV) from RNA-Seq data. Conceptually, MAJIQ/Voila can be divided into
- MAJIQ Builder: Uses RNA-Seq (BAM files) and a transcriptome annotation file (GFF3) to
define splice graphs and known/novel Local Splice Variations (LSV).
- MAJIQ Quantifier: Quantifies relative abundance (PSI) of LSVs and changes in relative LSV abundance
(delta PSI) between conditions w/wo replicates.
Voila: A visualization package that combines the output of MAJIQ Builder and MAJIQ Quantifier using
interactive D3 components and HTML5. Voila creates interactive summary files with gene splice graphs,
LSVs, and their quantification.
A web-tool for interpretation and downstream analysis of MAJIQ’s LSVs. Aids in visualizing and quantifying local isoform variations created by an LSV, RT-PCR primer design for experimental validation, and downstream functional analysis through connections to UCSC Genome Browser.
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- Dec 11, 2017 - Extensive evaluation of MAJIQ vs. LeafCutter, with analysis of recent LeafCutter paper.
- Dec 11, 2017 - New MAJIQ paper is out Norton and Vaquero-Garcia et al 2017. It describes a new module to improve the robustness of PSI quantification on experiments with outlier replicates. Also includes extensive comparisons to other software - rMATS, SUPPA2, and DEXSeq.
- Jul 29, 2017 - Posted videos along with examples and sample data of a recent workshop we ran for Splicing analysis using RNASeq data and MAJIQ.
- Sept 11, 2017 - MAJIQ-SPEL is released. This is a new web-tool for aiding researcher in validating splicing variations identified using MAJIQ. It includes automated experimental RT-PCR primer design tool. For more details see our recent Application Note published in Bioinformatics.