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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Updated: Jul 19, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data.

Dmitry Meleshko^1,2, Andrey D Prjbelski³, Mikhail Raiko⁴

¹Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, NY, 10021, USA.

Biorxiv : the Preprint Server for Biology

|August 7, 2023

Summary

This summary is machine-generated.

We developed cloudrnaSPAdes, a novel RNA sequencing assembler. This tool accurately reconstructs full-length RNA isoforms from barcoded linked-read data, addressing limitations of previous methods for isoform discovery.

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Last Updated: Jul 19, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

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Published on: January 10, 2019

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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

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Published on: August 20, 2021

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Long-read RNA sequencing offers full-length isoform analysis, but can be low coverage.
Barcoded short-read RNA sequencing (e.g., 10x Genomics linked-reads) provides an alternative for high-coverage isoform studies.
Existing pipelines struggle with barcoded short-read data and coverage gaps.

Conclusions:

cloudrnaSPAdes provides a valuable solution for assembling isoforms from barcoded RNA-seq data.
This advancement facilitates high-coverage, reference-free isoform discovery.
The tool enhances the utility of barcoded RNA-seq for comprehensive transcriptomic analysis.