Splicing and Junction Mapping

CLASS – Splice Variant Annotation from RNA-Seq Reads

rna-seq

Next generation sequencing of cellular RNA is making it possible to characterize genes and alternative splicing in unprecedented detail. However, designing bioinformatics tools to capture splicing variation accurately has proven difficult. Current programs find major isoforms of a gene but ...

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Open-access synthetic spike-in mRNA-seq data for cancer gene fusions

rna-seq

Oncogenic fusion genes underlie the mechanism of several common cancers. Next-generation sequencing based RNA-seq analyses have revealed an increasing number of recurrent fusions in a variety of cancers. However, absence of a publicly available gene-fusion focused RNA-seq data impedes comparative ...

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SUPPA – a super-fast pipeline for alternative splicing analysis from RNA-Seq

rna-seq

High-throughput RNA sequencing allows genome-wide analyses of pre-mRNA splicing across multiple conditions. However, the increasing number of available datasets represents a major challenge in terms of time and storage required for analyses. Now, a team led by researchers at the ...

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Pegasus – a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer

rna-seq

The extraordinary success of imatinib in the treatment of BCR-ABL1 associated cancers underscores the need to identify novel functional gene fusions in cancer. RNA sequencing offers a genome-wide view of expressed transcripts, uncovering biologically functional gene fusions. Although several bioinformatics ...

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RVboost: RNA-Seq variants prioritization using a boosting method

rna-seq

RNA-Seq has become the method of choice to quantify genes and exons, discover novel transcripts, and detect fusion genes. However, reliable variant identification from RNA-Seq data remains challenging due to the complexities of the transcriptome, the challenges of accurately mapping ...

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sQTLseekeR – Identification of genetic variants associated with alternative splicing

rna-seq

Identification of genetic variants affecting splicing in RNA sequencing population studies is still in its infancy. Splicing phenotype is more complex than gene expression and ought to be treated as a multivariate phenotype to be recapitulated completely. Here a team ...

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SLaP Mapper: a webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage

rna-seq

The Kinetoplastida are a diverse and globally distributed class of free-living and parasitic single-celled eukaryotes that collectively cause a significant burden on human health and welfare. In kinetoplastids individual genes do not have promoters, but rather all genes are arranged ...

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JAGuaR: Junction Alignments to Genome for RNA-Seq Reads

rna-seq

JAGuaR is an alignment protocol for RNA-seq reads that uses an extended reference to increase alignment sensitivity. It uses BWA to align reads to the genome and reference transcript models (including annotated exon-exon junctions) specifically allowing for the possibility of ...

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