Junction Usage Model (JUM) is a tool that offers a completely annotation-free approach to perform differential analysis of tissue-specific pre-mRNA alternative splicing patterns.
JUM takes in RNA-seq data prepared from different tissues/cell samples and output alternative splicing events in six categories (cassette exon, mutually exclusive exons, alternative 5' splice site, alternative 3' splice site, intron retention, Composite patterns) that are significantly altered due to a specific treatment, or difference in tissue types, etc.
JUM does not depend on any prior knowledge of the transcriptome/annotation libraries of AS events.
The analysis functions in the current version are complete. I will continue to simplify the user-interface.
Please refer to the JUM Wiki page for a complete and updated manual/guide https://github.com/qqwang-berkeley/JUM/wiki/A-Hitchhiker's-guide-to-JUM-(version-1.3.12-and-up)
A description of the JUM method is deposited to bioRxiv here (manuscript has been updated in May): https://www.biorxiv.org/content/early/2018/05/09/116863
Please contact me for any questions and comments.