Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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 microarray-based...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Triple Synergistic Modulation via Sn Doping in Tetrahedrites: Electronic Structure, DOS, and Scattering Engineering for a High Thermoelectric Performance.

ACS applied materials & interfaces·2025

Same author

Effect of 1-DNJ on Oxidative Stress-Induced Apoptosis in Porcine Ovarian GCs Through Modulation of the PERK-ATF4/MFN2 Signaling Pathway.

Antioxidants (Basel, Switzerland)·2025

Same author

Large-sized aerobic granular biofilm: stable biotechnology to improve nitrogen removal and reduce sludge yield.

Bioresource technology·2025

Same author

Effects of acceptance and commitment therapy plus exercise for older adults with chronic low back pain: A preliminary cluster randomized controlled trial with qualitative interviews.

The journal of pain·2025

Same author

Precisely tuning the electronic states of organic polymer electrocatalysts via thiophene-based moieties for enhanced oxygen reduction reaction.

iScience·2025

Same author

Design of self-assembled micelles based on natural dual-targeting strategies and evaluation of their anti-liver cancer effects as drug delivery systems.

NPJ precision oncology·2025

Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 9, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Short read mapping for exome sequencing.

Xueya Zhou¹, Suying Bao, Binbin Wang

¹Bioinformatics Division, Tsinghua National Laboratory of Information Science and Technology, Beijing, China.

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

|July 23, 2013

Summary

This summary is machine-generated.

This chapter details practical read mapping procedures for next-generation sequencing data. It addresses common challenges in building computational pipelines for exome sequencing studies.

More Related Videos

Methyl-binding DNA capture Sequencing for Patient Tissues

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

Related Experiment Videos

Last Updated: May 9, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Methyl-binding DNA capture Sequencing for Patient Tissues

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Next-generation sequencing (NGS) technologies are crucial for modern biological research.
Mapping short reads to a reference genome is a fundamental step in most NGS-based analyses.
Existing read mapping tools present practical challenges when integrated into computational workflows.

Purpose of the Study:

To illustrate practical considerations and procedures for short read mapping in exome sequencing.
To provide insights into building robust computational pipelines for genomic data analysis.
To address common issues encountered during the read mapping process.

Main Methods:

Description of read mapping protocols utilized in a specific laboratory setting.
Focus on exome sequencing studies as a representative example.
Discussion of practical details relevant to computational pipeline construction.

Main Results:

Identification of key practical issues in read mapping for NGS data.
Demonstration of a specific laboratory's approach to address these issues.
Illustrative examples of read mapping procedures in exome sequencing.

Conclusions:

Effective read mapping is critical for successful downstream NGS applications.
Addressing practical challenges in read mapping is essential for reliable computational pipelines.
The described procedures offer a practical framework for exome sequencing data analysis.