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Le RNA-seq. L  ’ article fondateur: Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008 320:1344-1349. En un run, on générait en 2011 environ 15 million de séquences de 35 bp.

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Presentation Transcript
slide2

L ’article fondateur:

Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008 320:1344-1349

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En un run, on générait en 2011 environ 15 million de séquences de 35 bp.

En 2012, en un run, on génère 1.6 milliard de séquences de 100 bp.

De plus on simplifie le protocole de réalisation des librairies.

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ERANGE

20 kpb

Le logiciel « maison » de Solexa écarte les « multireads »

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D’autres logiciels existants:

Bowtie (alignement)

TopHat (calcul RKPM)

Cufflink (calcul gene expression)

HTSeq: Analysing high-throughput sequencing data with Python

Une plateforme d’analyse de ces données: Galaxy:

http://main.g2.bx.psu.edu/

Un pipe d’analyse « standard »:

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Pour des méthodes plus sophistiquées de détection de transcrits, cf cours de Vincent Lacroix