Splicing and Junction Mapping

Micro-dissection and integration of long and short reads for identifying isoforms at microscopic structure-level

Studying isoform expression at the microscopic level has always been a challenging task. A classical...
Slinker – visualising novel splicing events in RNA-Seq data

Visualisation of the transcriptome relative to a reference genome is fraught with sparsity. This is ...
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 biologica...
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 select...
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 th...

Micro-dissection and integration of long and short reads for identifying isoforms at microscopic structure-level

April 27, 2022 Leave a comment 578 Views

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...

Slinker – visualising novel splicing events in RNA-Seq data

December 9, 2021 Leave a comment 1,330 Views

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...

New RNA-Seq mapping pipeline reveals the landscape of coding RNA editing events in pediatric cancer

November 19, 2021 Leave a comment 1,397 Views

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...

LR-Split-seq – mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution

April 28, 2021 Leave a comment 2,566 Views

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 ...

AS-Quant – Detection and Visualization of Alternative Splicing Events with RNA-seq Data

April 26, 2021 Leave a comment 2,478 Views

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.

FUNGI – Fusion Gene Integration Toolset

March 31, 2021 Leave a comment 1,730 Views

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...

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing

March 2, 2021 Leave a comment 1,376 Views

Transcription of eukaryotic genomes involves complex alternative processing of RNAs. Sequencing of full-length RNAs using long reads reveals the...

McSplicer – a probabilistic model for estimating splice site usage from RNA-seq data

February 2, 2021 Leave a comment 1,747 Views

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...

Arriba – accurate and efficient detection of gene fusions from RNA sequencing data

January 15, 2021 Leave a comment 2,776 Views

The identification of gene fusions from RNA sequencing data is a routine task in cancer research and precision oncology. However, despite the...

MetaTX -new model solves problem of isoform ambiguity

November 4, 2020 Leave a comment 1,750 Views

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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RNA-Seq Blog Transcriptome Research & Industry News

Splicing and Junction Mapping

Micro-dissection and integration of long and short reads for identifying isoforms at microscopic structure-level

Slinker – visualising novel splicing events in RNA-Seq data

New RNA-Seq mapping pipeline reveals the landscape of coding RNA editing events in pediatric cancer

LR-Split-seq – mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution

AS-Quant – Detection and Visualization of Alternative Splicing Events with RNA-seq Data

Micro-dissection and integration of long and short reads for identifying isoforms at microscopic structure-level

Slinker – visualising novel splicing events in RNA-Seq data

New RNA-Seq mapping pipeline reveals the landscape of coding RNA editing events in pediatric cancer

LR-Split-seq – mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution

AS-Quant – Detection and Visualization of Alternative Splicing Events with RNA-seq Data

FUNGI – Fusion Gene Integration Toolset

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing

McSplicer – a probabilistic model for estimating splice site usage from RNA-seq data

Arriba – accurate and efficient detection of gene fusions from RNA sequencing data

MetaTX -new model solves problem of isoform ambiguity

RPKM, FPKM and TPM, clearly explained

How to Analyze RNA-Seq Data?

Visualization of nucleotide substitutions in the (micro)transcriptome

Comparison of TMM (edgeR), RLE (DESeq2), and MRN Normalization Methods

An RNA-Seq QC Overview

STRIDE – a topic-model-based method to deconvolve spatial transcriptomics using scRNA-seq

Researchers find heart failure arises from mutations in numerous distinct genes

Transcriptome diversity in human tissues mapped with emerging long-read RNA sequencing technology

Significance analysis for clustering with single-cell RNA-sequencing data

BacDrop – droplet-based single-cell RNA-seq reveals heterogeneity in bacterial populations and in response to antibiotic perturbation

STRIDE – a topic-model-based method to deconvolve spatial transcriptomics using scRNA-seq

Researchers find heart failure arises from mutations in numerous distinct genes

Transcriptome diversity in human tissues mapped with emerging long-read RNA sequencing technology

Significance analysis for clustering with single-cell RNA-sequencing data

BacDrop – droplet-based single-cell RNA-seq reveals heterogeneity in bacterial populations and in response to antibiotic perturbation

Gruffi – an algorithm for improved delineation of developmental trajectories in organoids and resemblance to in vivo data.

Combi-seq – multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets