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================================================================<br>
<br>
-- ECCB 2014 Tutorial --<br>
Analysis of Cis-Regulatory Motifs from High-Throughput sequences<br>
<br>
================================================================<br>
<br>
<br>
There are still some places available for this tutorial:<br>
<br>
ECCB Tutorial T01<br>
Analysis of Cis-Regulatory Motifs from High-Throughput Sequence Sets<br>
<br>
Date: Saturday Sept 6, 2014<br>
Place: Forum building of the Faculty of Medicine of Strasbourg<br>
Time: 9am – 5.30pm (registration starts from 8am)<br>
<br>
Contact e-mail: <a href="mailto:mthomas@biologie.ens.fr">mthomas@biologie.ens.fr</a><br>
<br>
More details: <a href="http://www.eccb14.org/program/tutorials/cis-r">http://www.eccb14.org/program/tutorials/cis-r</a><br>
<br>
How to register: <a href="http://www.eccb14.org/registration">http://www.eccb14.org/registration</a><br>
<br>
Registration includes lunch & coffee breaks on the day of the workshop<br>
and the tutorial material (.pdf and/or print). ECCB Tutorial rates:<br>
110 € (academic) or 60 € (student)<br>
<br>
---------- Short description ----------<br>
<br>
This tutorial aims at introducing the theoretical principles and<br>
giving practical skills to use specialized software tools to extract<br>
motifs from full-scaled NGS datasets (typically covering tens of Mb).<br>
<br>
<br>
--------- Teachers ----------<br>
<br>
- Jacques van Helden, Aix-Marseille Université (France)<br>
- Morgane Thomas-Chollier, Ecole Normale Supérieure (France)<br>
- Carl Herrmann, University Heidelberg (Germany).<br>
- Alejandra Medina-Rivera, SickKids Research Institute, Toronto (Canada)<br>
<br>
---------- Description ----------<br>
<br>
Next Generation Sequencing led to the development of novel methods<br>
(ChIP-seq, FAIRE-seq, clip-seq, ) to acquire massive data about<br>
diverse signals involved in genome regulation and function<br>
(cis-regulation, chromatin conformation, RNA maturation,<br>
recombination, replication, ...).<br>
<br>
Extracting relevant information from the raw data requires not only<br>
specialized software tools, but also a good understanding of their<br>
principles and parameters.<br>
<br>
In this tutorial we will demonstrate how to analyze ChIP-seq data<br>
using the Regulatory Sequence Analysis Tools (RSAT,<br>
<a href="http://www.rsat.eu/">http://www.rsat.eu/</a>), via their different ways of access:<br>
web-interface, command-line, and web-services.<br>
<br>
This tutorial aims at introducing the theoretical principles and<br>
giving practical skills to use specialized software tools to extract<br>
motifs from full-scaled NGS datasets (typically covering tens of Mb).<br>
<br>
---------- Contents ----------<br>
<br>
The tutorial will be organized in 2 half days:<br>
<br>
1) Analysis of cis-regulatory elements with the Regulatory Sequence<br>
Analysis Tools (RSAT): methods and website utilization<br>
(<a href="http://www.rsat.eu/">http://www.rsat.eu/</a>).<br>
<br>
2) Using RSAT in command-line and via web services (SOAP/WSDL).<br>
<br>
Topics:<br>
- Motif discovery in NGS peak sets.<br>
- Impact of the background models.<br>
- Comparison between motifs.<br>
- Motif enrichment in peak sequences.<br>
- Evaluating the quality of motifs extracted from NGS peaks.<br>
- Building control sets to estimate the rates of false positives.<br>
<br>
---------- Topics not covered ----------<br>
<br>
Other steps for the analysis of ChIP-seq data (e.g. read mapping, peak<br>
calling, functional enrichment of peaks, other tools for pattern<br>
discovery and matching).<br>
<br>
---------- Target audience ----------<br>
<br>
The course is addressed to bioinformaticians and biologists. The<br>
afternoon will require being familiar with the Unix shell (Linux) and<br>
basic programming skills (Perl or Python) to implement clients for web<br>
services.<br>
<br>
---------- In practice ----------<br>
<br>
* Participants will need to bring their own laptop.<br>
<br>
* All command-line programs will be run on the IFB cloud platform<br>
(<a href="https://cloud.france-bioinformatique.fr/">https://cloud.france-bioinformatique.fr/</a>) managed by Christophe<br>
Blanchet (IBCP, Lyon, France). Each participant will be given a<br>
(free) account to access this cloud and thereby a fully functional<br>
virtual machine with RSAT.<br>
<br>
* Wireless internet will be available at the conference venue.<br>
<br>
* An indicative reading list will be available a few weeks before the<br>
tutorial.<br>
<br>
* The hands-on will be organized in a cookbook mode: we will<br>
distribute protocols explaining the steps to solve selected test<br>
cases.<br>
<br>
* For the practicals, we ensure that there is no need to transfer data<br>
from the conference room to the servers.<br>
<br>
---------- Funding ----------<br>
<br>
This tutorial is funded by the ALLBIO project<br>
(<a href="http://www.allbioinformatics.eu/">http://www.allbioinformatics.eu/</a>), whose goal is to establish the<br>
link between bioinformatics and biologist communities who express<br>
uncovered needs for other fields than human genomics (microbial,<br>
plant, livestock).<br>
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