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Le RNA-seq

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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Le RNA-seq

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  1. Le RNA-seq

  2. 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

  3. 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.

  4. Analyse des données: compter les gènes (transcrits)

  5. RKPM: reads per kilobase of exon model per million mappedreads

  6. ERANGE 20 kpb Le logiciel « maison » de Solexa écarte les « multireads »

  7. 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 »:

  8. TopHat is a fast splice junction mapper

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

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