Splicing and Junction Mapping

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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