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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: Aug 12, 2025

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Published on: December 14, 2017

Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores.

Luca Cozzuto¹, Anna Delgado-Tejedor^1,2, Toni Hermoso Pulido¹

¹Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.

Methods in Molecular Biology (Clifton, N.J.)

|February 1, 2023

Summary

This summary is machine-generated.

MasterOfPores v.2 (MoP2) is an open-source pipeline for direct RNA sequencing data analysis. This tool enables reproducible transcriptomic and epitranscriptomic studies using Oxford Nanopore technology.

Keywords:

Data analysis Direct RNA sequencing Nanopore sequencing Nextflow Open source RNA modifications Reproducible science Workflows

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Last Updated: Aug 12, 2025

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Published on: December 14, 2017

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

Direct RNA sequencing offers insights into RNA modifications and poly(A) tail dynamics.
Reproducible and efficient analysis pipelines are crucial for transcriptomic and epitranscriptomic research.

Purpose of the Study:

To introduce MasterOfPores v.2 (MoP2), an open-source bioinformatics pipeline.
To provide a reproducible workflow for processing and analyzing direct RNA Oxford Nanopore sequencing data.

Main Methods:

MoP2 utilizes the Nextflow DSL2 framework and Linux containers for reproducible analysis.
The workflow includes pre-processing (basecalling, quality control, demultiplexing, filtering, mapping), abundance estimation, and transcriptome assembly.
GPU computing support is integrated for basecalling and demultiplexing.

Main Results:

The pipeline facilitates the estimation of RNA poly(A) tail lengths.
MoP2 enables the identification of RNA modifications from direct RNA sequencing data.
A fully reproducible example using S. cerevisiae total RNA is provided.

Conclusions:

MoP2 provides a robust and reproducible solution for direct RNA sequencing data analysis.
The pipeline supports comprehensive transcriptomic and epitranscriptomic investigations.
MoP2 is available as open-source software, promoting accessibility and collaboration.