Studying isoform expression at the microscopic level has always been a challenging task. A classical example is kidney, where glomerular and tubulo-interstitial compartments carry out drastically different...
Read More »Slinker – visualising novel splicing events in RNA-Seq data
Visualisation of the transcriptome relative to a reference genome is fraught with sparsity. This is due to RNA sequencing (RNA-Seq) reads being predominantly mapped to exons that account for...
Read More »New RNA-Seq mapping pipeline reveals the landscape of coding RNA editing events in pediatric cancer
RNA editing leads to post-transcriptional variation in protein sequences and has important biological implications. Researchers from the St. Jude Children’s Research Hospital sought to elucidate the...
Read More »LR-Split-seq – mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution
Alternative RNA isoforms are defined by promoter choice, alternative splicing, and polyA site selection. Although differential isoform expression is known to play a large regulatory role in eukaryotes, it has proved challenging to study with standard short-read RNA-seq because of ...
Read More »AS-Quant – Detection and Visualization of Alternative Splicing Events with RNA-seq Data
A simplistic understanding of the central dogma falls short in correlating the number of genes in the genome to the number of proteins in the proteome.
Read More »FUNGI – Fusion Gene Integration Toolset
Fusion genes are both useful cancer biomarkers and important drug targets. Finding relevant fusion genes is challenging due to genomic instability resulting in a high number of passenger events...
Read More »2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing
Transcription of eukaryotic genomes involves complex alternative processing of RNAs. Sequencing of full-length RNAs using long reads reveals the...
Read More »McSplicer – a probabilistic model for estimating splice site usage from RNA-seq data
Alternative splicing removes intronic sequences from transcripts in alternative ways to produce different forms (isoforms) of mature mRNA. The composition of expressed transcripts and their alternative forms give specific functionalities to cells in a particular...
Read More »Arriba – accurate and efficient detection of gene fusions from RNA sequencing data
The identification of gene fusions from RNA sequencing data is a routine task in cancer research and precision oncology. However, despite the...
Read More »MetaTX -new model solves problem of isoform ambiguity
A new statistical model from Xi’an Jiaotong-Liverpool University aims to solve the problem of isoform ambiguity related to RNA modifications. The paper, published on 2 November in the leading...
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