Tag Archives: junction mapping

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Accurate detection of differential RNA processing

Deep transcriptome sequencing (RNA-Seq) has become a vital tool for studying the state of cells in the context of varying environments, genotypes and other factors. RNA-Seq profiling data enable identification of novel isoforms, quantification of known isoforms and detection of ...

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Methods to Study Splicing from RNA-Seq

from figshare – by Eduardo Eyras, Gael P. Alamancos & Eneritz Agirre Graphical representation of methods to study splicing from RNA-Seq. Methods are divided according to whether they perform Mapping, Reconstruction of events or isoforms, Quantification of events and/or isoforms ...

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Intron-Centric Estimation of Alternative Splicing from RNA-seq data

Novel technologies brought in unprecedented amounts of high-throughput sequencing data along with great challenges in their analysis and interpretation. The percent-spliced-in (PSI, Ψ) metric estimates the incidence of single-exon skipping events and can be computed directly by counting reads that ...

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JETTA: Junction and Exon Toolkits for Transcriptome Analysis

JETTA detects alternatively spliced exons based on pre-calculated statistics of exons and junctions in RNA-Seq data sets. It does not support low-level RNA-Seq analysis such as base calling, mapping, alignment, transcript assembly, and expression calculation. For low-level RNA-Seq analysis, please ...

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SpliceTrap – a method to quantify alternative splicing

SpliceTrap is a method to quantify exon inclusion levels using paired-end RNA-seq data. Unlike other tools, which focus on full-length transcript isoforms, SpliceTrap approaches the expression-level estimation of each exon as an independent Bayesian inference problem. In addition, SpliceTrap can ...

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