Tutorial: Rna-Seq Review Papers
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gravatar for Istvan Albert
7.0 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

Review papers on the topic of RNA-seq

General Guides

Tophat and Cufflinks

Tophat is a tool to align RNA-seq reads, Cufflinks assembles transcripts, and estimates their abundances

Transcriptome Assembly

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rna-seq papers tutorial • 20k views
ADD COMMENTlink modified 3.5 years ago by art.matysik0 • written 7.0 years ago by Istvan Albert ♦♦ 81k
3

Here is a review/educational paper "Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud" that accompanies an extensive hands-on tutorial at rnaseq.wiki. It covers many aspects of RNA-seq and includes primers on related fundamentals that you will need including Unix, R, Genome Browsers, using cloud computing, etc.

ADD REPLYlink written 3.8 years ago by Malachi Griffith17k
1

Update 2016;

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8

ADD REPLYlink written 3.5 years ago by Medhat8.4k
5
gravatar for NextGenSeek
7.0 years ago by
NextGenSeek290
NextGenSeek290 wrote:

Here is more.

RNA-Seq: a revolutionary tool for transcriptomics. Zhong Wang, Mark Gerstein & Michael Snyder, Nature Reviews Genetics 10, 57-63 (January 2009)

Next-generation transcriptome assembly. Jeffrey A. Martin & Zhong Wang Nature Reviews Genetics 12, 671-682 (October 2011)

RNA sequencing: advances, challenges and opportunities Fatih Ozsolak & Patrice M. Milos, Nature Reviews Genetics 12, 87-98 (February 2011)

RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing Brian T. Wilhelma and Josette-Renée Landryb, Methods Volume 48, Issue 3, July 2009, Pages 249–257

ADD COMMENTlink modified 7.0 years ago • written 7.0 years ago by NextGenSeek290

I am going to add the checkmark to any post that is merged into the toplevel one

ADD REPLYlink written 7.0 years ago by Istvan Albert ♦♦ 81k
1
gravatar for NextGenSeek
7.0 years ago by
NextGenSeek290
NextGenSeek290 wrote:

Models for transcript quantification from RNA-Seq, Lior Pachter, preprint arXiv 2012

Computation for ChIP-seq and RNA-seq studies. Pepke, Shirley; Wold, Barbara; Mortazavi, Ali, Nature methods. 2009 6(11 Suppl):S22-32

ADD COMMENTlink modified 7.0 years ago • written 7.0 years ago by NextGenSeek290
1
gravatar for upendrakumar.devisetty
6.8 years ago by
United States
upendrakumar.devisetty350 wrote:

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA‐seq experiments

Molecular Ecology

Nagarjun Vijay Jelmer W. Poelstra Axel Künstner Jochen B. W. Wolf

RNA-Seq Assembly – Are We There Yet?

Simon Schliesky,1 Udo Gowik,2 Andreas P. M. Weber,1 and Andrea Bräutigam1,*

ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by upendrakumar.devisetty350
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