Splicing and Junction Mapping

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Designing alternative splicing RNA-seq studies

Designing alternative splicing RNA-seq studies

esigning an RNA-seq study depends critically on its specific goals, technology and underlying biology, which renders general guidelines inadequate.  A team led by researchers at IRB Barcelona have developed a Bayesian framework to customize experiments so that goals can be ...

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Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

Alternative splicing shapes mammalian transcriptomes, with many RNA molecules undergoing multiple distant alternative splicing events. Comprehensive transcriptome analysis, including analysis of exon co-association in the same molecule, requires deep, long-read sequencing. Here we introduce an RNA sequencing method, synthetic long-read ...

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Rail-RNA – Scalable analysis of RNA-seq splicing and coverage

Rail-RNA – Scalable analysis of RNA-seq splicing and coverage

RNA sequencing (RNA-seq) experiments now span hundreds to thousands of samples. A source of frustration for investigators analyzing a given dataset is the inability to rapidly and reproducibly align its samples jointly. Current spliced alignment software is designed to analyze ...

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Quantification of co-transcriptional splicing from RNA-Seq data

Quantification of co-transcriptional splicing from RNA-Seq data

During gene expression, protein-coding transcripts are shaped by multiple processing events: 5′ end capping, pre-mRNA splicing, RNA editing, and 3′ end cleavage and polyadenylation. These events are required to produce mature mRNA, which can be subsequently translated. Nearly all of ...

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