From RNA-Seq data to bioinformatics analysis using Nanopore sequencers

December 13, 2017, Genoscope, Evry
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This one-day workshop is dedicated to transcriptome studies using the MinION. This sequencer can generate fragments up to hundreds of kilobases, and has the ability to perform full-length sequencing of RNA strands directly, or of cDNA. It opens up new perspectives to decipher the structure of genes and estimate their expression both at the gene and isoform level. It also raises a number of bioinformatics challenges to analyse the data. The goal of this meeting is to share recent experiences and results on these topics. The workshop is organized by members of the ASTER Project and funded by France Génomique and Oxford Nanopore company.

Slides can be found on the following web site : RNA workshop slides


10:00 - 10:40 Registration and welcome coffee
10:40 - 10:45 Introduction
10:45 - 11:30 James Platt (Oxford Nanopore), Full length transcript sequencing of RNA and cDNA with Oxford Nanopore.
11:30 - 12:00 Jean-Marc Aury (Genoscope), RNA sequencing with the MinION at Genoscope.
12:00 - 12:45Laurent Jourdren and Sophie Lemoine (IBENS Paris), One year of developments and collaborations around the MinION on the Genomic facility of the IBENS.

12:45 - 14:00 Lunch and open discussions

14:00 - 14:30 Quentin Carradec (Genoscope), MinION on board of the Tara expedition
14:30 - 15:00 Rayan Chikhi (CNRS, CRIStAL, Lille) and Leandro Lima (ERABLE, Lyon), A first look at error-correction tools on Nanopore RNA-seq data
15:00 - 15:45 Hagen Tilgner (BRMI, Weill Cornell), What genes are saying, not how much they talk
15:45-16:30 Coffee break
16:30- 17:00 Vincent Lacroix (ERABLE, Lyon), Identification and quantification of isoforms in RNAseq data: deep short reads Vs shallow long reads: initial answers and open questions
17:00- 17:30 Camille Marchet (IRISA Rennes), De novo Clustering of Gene Expressed Variants in Transcriptomic Long Reads Data Sets

The organizers:
Hélène Touzet (CNRS, CRIStAL, Lille)
Vincent Lacroix (ERABLE, Lyon)
Jean-Marc Aury (Genoscope, Evry)