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Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

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Published on: September 16, 2019

Handling multi-mapped reads in RNA-seq.

Gabrielle Deschamps-Francoeur¹, Joël Simoneau¹, Michelle S Scott¹

¹Département de Biochimie et Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.

Computational and Structural Biotechnology Journal

|July 9, 2020

Summary

This summary is machine-generated.

Eukaryotic genomes contain many duplicated sequences that complicate RNA sequencing (RNA-seq) analysis. This review explores computational strategies to accurately quantify gene and transcript abundance despite these challenges.

Keywords:

Duplicated genes Expectation–maximization algorithm Gene isoforms Multi-mapped reads Noncoding RNAs RNA-seq

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A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Eukaryotic genomes are rich in duplicated sequences arising from various mechanisms like recombination and retrotransposition.
These repetitive elements complicate accurate gene and transcript quantification in RNA sequencing (RNA-seq) due to multi-mapped reads.
Different RNA biotypes exhibit varying degrees of sequence duplication, impacting quantification strategies.

Purpose of the Study:

To review the mechanisms driving sequence duplication in eukaryotic genomes.
To discuss the impact of duplicated sequences on RNA-seq analysis and gene quantification.
To explore existing and needed computational strategies for handling multi-mapped reads.

Main Methods:

Literature review of studies on genome duplication and RNA-seq analysis.
Analysis of computational approaches for multi-mapped read resolution.
Comparison of strategies for short and long RNA biotype quantification.

Main Results:

Sequence duplication arises from recombination, whole genome duplication, and retrotransposition.
Multi-mapped reads from repetitive sequences pose significant challenges for accurate gene/transcript quantification.
Dissimilar sequence similarity across RNA biotypes necessitates distinct quantification tools.

Conclusions:

Effective handling of multi-mapped reads is crucial for improving RNA-seq quantification accuracy.
Further development of computational tools is needed to address the complexities of duplicated sequences in diverse RNA biotypes.
Overcoming challenges in quantifying genes within repetitive genomic regions remains an active area of research.