A beginner’s guide to analysis of RNA sequencing data

Clarissa M. Koch, Stephen F. Chiu, Mahzad Akbarpour, Ankit Bharat, Karen M Ridge, Elizabeth Thomas Bartom, Deborah Rachelle Winter

Research output: Contribution to journalReview article

2 Citations (Scopus)

Abstract

Since the first publications coining the term RNA-seq (RNA sequencing) appeared in 2008, the number of publications containing RNA-seq data has grown exponentially, hitting an all-time high of 2,808 publications in 2016 (PubMed). With this wealth of RNA-seq data being generated, it is a challenge to extract maximal meaning from these datasets, and without the appropriate skills and background, there is risk of misinterpretation of these data. However, a general understanding of the principles underlying each step of RNA-seq data analysis allows investigators without a background in programming and bioinformatics to critically analyze their own datasets as well as published data. Our goals in the present review are to break down the steps of a typical RNA-seq analysis and to highlight the pitfalls and checkpoints along the way that are vital for bench scientists and biomedical researchers performing experiments that use RNA-seq.

Original languageEnglish (US)
Pages (from-to)145-157
Number of pages13
JournalAmerican journal of respiratory cell and molecular biology
Volume59
Issue number2
DOIs
StatePublished - Aug 1 2018

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RNA Sequence Analysis
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Keywords

  • Bioinformatics
  • Data analysis
  • RNA sequencing
  • Transcriptomics

ASJC Scopus subject areas

  • Molecular Biology
  • Pulmonary and Respiratory Medicine
  • Clinical Biochemistry
  • Cell Biology

Cite this

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A beginner’s guide to analysis of RNA sequencing data. / Koch, Clarissa M.; Chiu, Stephen F.; Akbarpour, Mahzad; Bharat, Ankit; Ridge, Karen M; Bartom, Elizabeth Thomas; Winter, Deborah Rachelle.

In: American journal of respiratory cell and molecular biology, Vol. 59, No. 2, 01.08.2018, p. 145-157.

Research output: Contribution to journalReview article

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AU - Koch, Clarissa M.

AU - Chiu, Stephen F.

AU - Akbarpour, Mahzad

AU - Bharat, Ankit

AU - Ridge, Karen M

AU - Bartom, Elizabeth Thomas

AU - Winter, Deborah Rachelle

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