A survey of best practices for RNA-seq data analysis.

Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J Gaffney, Laura L Elo, Xuegong Zhang, Ali Mortazavi

January 2016 Genome Biol

Synopsis of Social media discussions

Discussions around the article often emphasize its role as a foundational resource for RNA-seq data analysis. For example, several contributors remarked on its value for beginners, using phrases like 'best start for people who want to learn bulk transcriptomics,' which conveys the article's educational potential. Other posts mentioned its selection as one of the most accessed papers, reinforcing its high perceived impact in the scientific community.

A
Agreement
 Strong agreement

The majority of discussions reflect strong agreement with the methodologies and findings presented in the article, highlighting their importance.

I
Interest
 High level of interest

There is a high level of interest shown, with many contributors eager to explore the practices and techniques mentioned in the publication.

E
Engagement
 Moderate level of engagement

Engagement is somewhat moderate, with some posts providing examples and referring to specific methodologies without extensive discussion.

I
Impact
 High level of impact

Many users believe this article will have a significant influence on best practices for RNA-seq analysis.

Social Mentions

YouTube

3 Videos

Facebook

14 Posts

Twitter

56 Posts

Blogs

5 Articles

News

2 Articles

Reddit

2 Posts

Metrics

Video Views

117

Total Likes

129

Extended Reach

294,119

Social Features

82

Timeline: Posts about article

Top Social Media Posts

Posts referencing the article

Best Practices for RNA-Sequencing Data Analysis

Best Practices for RNA-Sequencing Data Analysis

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May 6, 2025

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Best Practices for RNA-seq Data Analysis

Best Practices for RNA-seq Data Analysis

This video provides a survey of best practices for RNA-seq data analysis, an essential tool for studying gene expression. It covers crucial steps from experimental design to functional analysis, while addressing challenges and exploring small RNA analysis and future advancements in transcriptomics.

豆豆

January 13, 2023

17 views

Best Practices in RNA-seq Data Analysis: A Comprehensive Guide

Best Practices in RNA-seq Data Analysis: A Comprehensive Guide

RNA-sequencing (RNA-seq) is a versatile tool used for studying gene expression and requires a tailored analysis pipeline for different applications. This review covers essential steps in RNA-seq data analysis, addressing challenges while exploring future advancements in transcriptomics technology.

Bioinfo Cafe (バイオインフォ カフェ)

May 10, 2025

12 views

  • Martin Paliocha
    @paliocha (Twitter)

    @BullCrys Start reading this? https://t.co/qkuqQuMd5q
    view full post

    February 13, 2024

    2

  • Aloo Vicc TO
    @AloVicky_HG (Twitter)

    RT @wintergenomics: Este estudio describe los pasos principales en el análisis de datos de #RNAseq: control de calidad, alineación de lectu…
    view full post

    April 18, 2023

    1

  • Winter Genomics
    @wintergenomics (Twitter)

    Este estudio describe los pasos principales en el análisis de datos de #RNAseq: control de calidad, alineación de lecturas, cuantificación de los niveles de genes y transcritos, visualización, lmapeo de #eQTL entre otros. Info: https://t.co/ZGIaqs6PhV https://t.co/RZkhVrDgrc
    view full post

    April 18, 2023

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    1

  • Burak Kahveci
    @burakkahveci_ (Twitter)

    @MoLOTSofScience You can look this links. https://t.co/iq3isRI5YF https://t.co/igUCcJGgsg Also, this paper is the best for the beginners https://t.co/ajk4aUEDWu
    view full post

    February 24, 2023

    2

  • Pedro Madrigal
    @compBiology (Twitter)

    RT @burakkahveci_: There are some papers that you can learn new things each reading. Here is one such paper. I think this paper provides on…
    view full post

    November 5, 2022

    5

  • Omicdata
    @omicdata (Twitter)

    RT @burakkahveci_: There are some papers that you can learn new things each reading. Here is one such paper. I think this paper provides on…
    view full post

    October 6, 2022

    5

  • Pierre Poulain
    @pierrepo (Twitter)

    RT @burakkahveci_: There are some papers that you can learn new things each reading. Here is one such paper. I think this paper provides on…
    view full post

    October 6, 2022

    5

  • Bioinformatics Trends 
    @BinfoTrends (Twitter)

    RT @burakkahveci_: There are some papers that you can learn new things each reading. Here is one such paper. I think this paper provides on…
    view full post

    October 6, 2022

    5

  • CompChemBio Bot
    @CompChemBioBot (Twitter)

    RT @burakkahveci_: There are some papers that you can learn new things each reading. Here is one such paper. I think this paper provides on…
    view full post

    October 6, 2022

    5

  • Burak Kahveci
    @burakkahveci_ (Twitter)

    There are some papers that you can learn new things each reading. Here is one such paper. I think this paper provides one of the best start for people who want to learn bulk transcriptomics. https://t.co/ajk4aUEDWu #RNASeqAnalysis #transcriptomics #Bioinformatics
    view full post

    October 6, 2022

    9

    5

  • Inés Lucía Patop
    @inespatop (Twitter)

    @RamosNeuro A few on RNA vs Prot https://t.co/B2Dy6PwgPg https://t.co/M77ym7p9tD and on RNA seq interpret https://t.co/9w9BYlByyo
    view full post

    September 15, 2022

    5

  • Dalia K. M. Khojely
    @DaliaACA (Twitter)

    A survey of best practices for RNA-seq data analysis https://t.co/tRHHLmBM5D
    view full post

    June 7, 2022

  • Hec
    @Muscles_n_Mitos (Twitter)

    RT @metapredict: 2016: claimed n=3 was ok for calculating differential expression (across 10's of thousands of rows https://t.co/DLPybPJWep…
    view full post

    May 18, 2022

    1

  • Jamie Timmons
    @metapredict (Twitter)

    2016: claimed n=3 was ok for calculating differential expression (across 10's of thousands of rows https://t.co/DLPybPJWep) As implausible as that general advice might seem, in 2022 now DEseq2 and edgeR don't seem to work very well. What a surprise. https://t.co/K646SkONuu
    view full post

    May 18, 2022

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    1

  • James.D.B
    @JamesDB72801774 (Twitter)

    A survey of best practices for RNA-seq data analysis https://t.co/sa6X88WUBz
    view full post

    April 7, 2022

  • Scientific Cockroach
    @MVB_science (Twitter)

    @tanjaslotte Maybe a little older but still useful https://t.co/1miOCbxFB0
    view full post

    March 5, 2021

    2

  • Ali Mortazavi
    @calizavi (Twitter)

    RT @compBiology: Wow! Our review 'A survey of best practices for RNA-seq data analysis' was chosen by @GenomeBiology as one of the 20 most-…
    view full post

    August 18, 2020

    1

  • Pedro Madrigal
    @compBiology (Twitter)

    Wow! Our review 'A survey of best practices for RNA-seq data analysis' was chosen by @GenomeBiology as one of the 20 most-interesting/most-accessed papers of their first 20 years @ConesaLab @calizavi https://t.co/KGJKzIvYqY
    view full post

    August 18, 2020

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    1

  • Dr Shailesh Kumar, PhD, MTech
    @Shail2211 (Twitter)

    RT @CancerEvolution: A generic roadmap for RNA-seq computational analyses. The major analysis steps are listed above the lines for pre-anal…
    view full post

    February 1, 2020

    1

  • Arash Davari Serej
    @ireflectit (Twitter)

    A generic roadmap for RNA-seq computational analyses. The major analysis steps are listed above the lines for pre-analysis, core analysis and advanced analysis. Ref: A survey of best practices for RNA-seq data analysis (https://t.co/BSo3xrU0lU) #singlecell #rnaseq #scRNAseq https://t.co/Fp3meqFzJM
    view full post

    January 31, 2020

    3

    1

  • Pedro Madrigal
    @compBiology (Twitter)

    RT @bioinfo_mark: @bevthescientist Here’s a nice paper on best practices. Should get you going in the right direction. I’m also happy to…
    view full post

    December 24, 2019

    1

  • Mark T. W. Ebbert
    @bioinfo_mark (Twitter)

    @bevthescientist Here’s a nice paper on best practices. Should get you going in the right direction. I’m also happy to help. https://t.co/2DSLBRFxvj
    view full post

    December 19, 2019

    2

    1

  • BF Francis Ouellette
    @bffo (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 11, 2019

    14

  • Pedro Madrigal
    @compBiology (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 8, 2019

    14

  • Fabrice Leclerc
    @rnomics (Twitter)

    https://t.co/T4VNBBfqGo A survey of best practices for RNA-seq data analysis | Genome Biology | Full Text https://t.co/QW9KEqdtZ9 RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of th…
    view full post

    November 8, 2019

  • Fabrice Leclerc
    @rnomics (Twitter)

    https://t.co/rv12ewG5Um The Tweeted Times - personal newspaper generated from your Twitter account https://t.co/58icWrgPSa posted by friends:  (1) garrymyers: Top RNomics #tweeted story: A survey of best practices for RNA-seq data analysis | Genome Biology | Full Text genom…
    view full post

    November 8, 2019

  • Fabrice Leclerc
    @rnomics (Twitter)

    Top #tweeted story in #bioscience: A survey of best practices for RNA-seq data analysis | Genome Biology | Full Text https://t.co/nPNEzcRqbk, see more https://t.co/kME3G1o122
    view full post

    November 8, 2019

  • Hafiz
    @f1zzydoesmicro (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 8, 2019

    14

  • Fabrice Leclerc
    @rnomics (Twitter)

    Top @RNomics #tweeted story: A survey of best practices for RNA-seq data analysis | Genome Biology | Full Text https://t.co/nPNEzcRqbk, see more https://t.co/mx2YzvfCax
    view full post

    November 8, 2019

    3

  • Camille Marchet @CamilleMrcht@genomic.social
    @CamilleMrcht (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 8, 2019

    14

  • Fabrice Leclerc
    @rnomics (Twitter)

    A survey of best practices for RNA-seq data analysis | Genome Biology | Full Text https://t.co/T4VNBBfqGo https://t.co/QW9KEqdtZ9 RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of th…
    view full post

    November 8, 2019

  • GangWu
    @GangWu10 (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 7, 2019

    14

  • Athanasios (Athan) Zovoilis
    @ZovoilisLab (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 7, 2019

    14

  • GOBLET
    @mygobletorg (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 7, 2019

    14

  • H3ABioNet
    @H3ABioNet (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 7, 2019

    14

  • AnaConesa
    @anaconesa (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 7, 2019

    14

  • Alicia Oshlack
    @AliciaOshlack (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 7, 2019

    14

  • Amal Katrib (أمل قطريب)
    @AmalKatrib (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 7, 2019

    14

  • Jason "boundless delight " Williams
    @JasonWilliamsNY (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 7, 2019

    14

  • nextgenseek
    @nextgenseek (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 7, 2019

    14

  • จิตร์ทัศน์
    @jittat (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 7, 2019

    14

  • Genome Biology
    @GenomeBiology (Twitter)

    RT @lpachter: Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of…
    view full post

    November 7, 2019

    14

  • Lior Pachter
    @lpachter (Twitter)

    Start of the transcriptomics session at #gi2019. First speaker is @anaconesa who is the primary author (with @compBiology) of an influential review on best practices for RNA-seq: https://t.co/S0sJoFwBhK
    view full post

    November 7, 2019

    45

    14

  • Tito
    @tito_tasks (Twitter)

    RT @BioDecoded: A survey of best practices for RNA-seq data analysis | Genome Biology https://t.co/GJFb0BE8wE #RNAseq #bioinformtics https…
    view full post

    September 29, 2019

    1

  • BioDecoded
    @BioDecoded (Twitter)

    A survey of best practices for RNA-seq data analysis | Genome Biology https://t.co/GJFb0BE8wE #RNAseq #bioinformtics https://t.co/LUWPElhyHq
    view full post

    September 29, 2019

    6

    1

  • David Ashbrook
    @DavidAshbrook (Twitter)

    @SecondRatMom Off the top of my head, table 1 of this paper, which compares fold-change and power. https://t.co/MizmGVoZSa
    view full post

    August 12, 2019

    1

  • Anthony Mathelier
    @AMathelier (Twitter)

    RT @lpachter: @leon_anavy @flo_compbio @IgorUlitsky @RNASeqBlog This is a very good review by @anaconesa, @compBiology et al. https://t.co…
    view full post

    June 20, 2019

    7

  • GreiffLab
    @victorgreiff (Twitter)

    RT @lpachter: @leon_anavy @flo_compbio @IgorUlitsky @RNASeqBlog This is a very good review by @anaconesa, @compBiology et al. https://t.co…
    view full post

    June 20, 2019

    7

  • Jan Baumbach
    @janbaumbach (Twitter)

    RT @lpachter: @leon_anavy @flo_compbio @IgorUlitsky @RNASeqBlog This is a very good review by @anaconesa, @compBiology et al. https://t.co…
    view full post

    June 20, 2019

    7

  • Pedro Madrigal
    @compBiology (Twitter)

    RT @lpachter: @leon_anavy @flo_compbio @IgorUlitsky @RNASeqBlog This is a very good review by @anaconesa, @compBiology et al. https://t.co…
    view full post

    June 19, 2019

    7

  • Greg Szeto, @gregszeto@genomic.social
    @greg_szeto (Twitter)

    RT @lpachter: @leon_anavy @flo_compbio @IgorUlitsky @RNASeqBlog This is a very good review by @anaconesa, @compBiology et al. https://t.co…
    view full post

    June 19, 2019

    7

  • Lior Pachter
    @lpachter (Twitter)

    @leon_anavy @flo_compbio @IgorUlitsky @RNASeqBlog This is a very good review by @anaconesa, @compBiology et al. https://t.co/S0sJoFeZTa
    view full post

    June 19, 2019

    30

    7

  • Diego Forero MD, PhD
    @daforerog (Twitter)

    A survey of best practices for RNA-seq data analysis https://t.co/FsneqQ9XM4
    view full post

    May 6, 2019

    1

  • Miguel A. Minaya
    @miguel_minaya_ (Twitter)

    A cornerstone for RNA-seq data analyses!! A survey of best practices for RNA-seq data analysis https://t.co/n6DnTVij59
    view full post

    March 13, 2019

    1

  • Pedro Madrigal
    @compBiology (Twitter)

    RT @jmirobla: If you want to perform an RNAseq experiment properly, worth to check this review on best practices from @conesagroup @anacone…
    view full post

    January 14, 2019

    10

  • Samuel Abalde
    @saabalde (Twitter)

    RT @jmirobla: If you want to perform an RNAseq experiment properly, worth to check this review on best practices from @conesagroup @anacone…
    view full post

    January 10, 2019

    10

Abstract Synopsis

  • RNA-sequencing (RNA-seq) is a versatile tool used for studying gene expression and requires a tailored analysis pipeline for different applications.
  • The review covers essential steps in RNA-seq data analysis, from experimental design to functional analysis, while also addressing challenges encountered along the way.
  • The article also explores the analysis of small RNAs, integration with other techniques, and future advancements in transcriptomics technology.