Alternative splicing plays an essential role in many cellular processes and bears major relevance in the understanding of multiple diseases, including cancer. High-throughput RNA sequencing allows genome-wide analyses of splicing across multiple conditions. However, the increasing number of available data ...
Read More »JAFFA – High sensitivity transcriptome-focused fusion gene detection
Genomic instability is a hallmark of cancer and, as such, structural alterations and fusion genes are common events in the cancer landscape. RNA sequencing (RNA-Seq) is a powerful method for profiling cancers, but current methods for identifying fusion genes are ...
Read More »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 ...
Read More »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 ...
Read More »ESFinder – Identification of Exon Skipping Events from High-Throughput RNA Sequencing Data
The emergence of next-generation high-throughput RNA sequencing (RNA-Seq) provides tremendous opportunities for researchers to analyze alternative splicing on a genome-wide scale. However, accurate identification of alternative splicing events from RNA-Seq data has remained an unresolved challenge in next-generation sequencing (NGS) ...
Read More »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 ...
Read More »SplAdder – Identification, quantification and testing of alternative splicing events from RNA-Seq data
Understanding the occurrence and regulation of alternative splicing (AS) is a key task towards explaining the regulatory processes that help to shape the complex transcriptomes of higher eukaryotes. With the advent of high-throughput sequencing of RNA, the diversity of AS ...
Read More »SplicePie – a novel analytical approach for the detection of alternative, non-sequential and recursive splicing
Alternative splicing is a powerful mechanism present in eukaryotic cells to obtain a wide range of transcripts and protein isoforms from a relatively small number of genes. The mechanisms regulating (alternative) splicing and the paradigm of consecutive splicing have recently ...
Read More »Mapping Splicing Quantitative Trait Loci in RNA-Seq
One of the major mechanisms of generating mRNA diversity is alternative splicing, a regulated process that allows for the flexibility of producing functionally different proteins from the same genomic sequences. This process is often altered in cancer cells to produce ...
Read More »rSeqNP: A non-parametric approach for detecting differential expression and splicing from RNA-Seq data
High-throughput sequencing of transcriptomes (RNA-Seq) has become a powerful tool to study gene expression. Here researchers from the University of Michigan present an R package, rSeqNP, which implements a non-parametric approach to test for differential expression and splicing from RNA-Seq ...
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