nBioinformatics Pipeline for Transcriptome Sequencing Analysis - Université de Rennes Accéder directement au contenu
Chapitre D'ouvrage Année : 2017

nBioinformatics Pipeline for Transcriptome Sequencing Analysis

Résumé

The development of High Throughput Sequencing (HTS) for RNA profiling (RNA-seq) has shed light on the diversity of transcriptomes. While RNA-seq is becoming a de facto standard for monitoring the population of expressed transcripts in a given condition at a specific time, processing the huge amount of data it generates requires dedicated bioinformatics programs. Here, we describe a standard bioinformatics protocol using state-of-the-art tools, the STAR mapper to align reads onto a reference genome, Cufflinks to reconstruct the transcriptome, and RSEM to quantify expression levels of genes and transcripts. We present the workflow using human transcriptome sequencing data from two biological replicates of the K562 cell line produced as part of the ENCODE3 project.
Fichier non déposé

Dates et versions

hal-02788591 , version 1 (05-06-2020)

Identifiants

Citer

Sarah Djebali, Valentin Wucher, Sylvain Foissac, Christophe Hitte, Erwan Corre, et al.. nBioinformatics Pipeline for Transcriptome Sequencing Analysis. Enhancer RNAs : Methods and Protocols, 1468 (Chapter 14), Humana Press Inc., 2017, Methods in Molecular Biology, 978-1-4939-4033-2. ⟨10.1007/978-1-4939-4035-6_14⟩. ⟨hal-02788591⟩
25 Consultations
0 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More