[BBC] ECCB 2014 Tutorial : Analysis of Cis-Regulatory Motifs from High-Throughput

[Jacques van Helden]

There are still some places available for this tutorial:

ECCB Tutorial T01
Analysis of Cis-Regulatory Motifs from High-Throughput Sequence Sets

Date: Saturday Sept 6, 2014
Place: Forum building of the Faculty of Medicine of Strasbourg
Time: 9am – 5.30pm (registration starts from 8am)

Contact e-mail: mthomas at biologie.ens.fr

More details: http://www.eccb14.org/program/tutorials/cis-r

How to register: http://www.eccb14.org/registration

Registration includes lunch & coffee breaks on the day of the workshop
and the tutorial material (.pdf and/or print). ECCB Tutorial rates:
110 € (academic) or 60 € (student)

----------     Short description     ----------

This tutorial aims at introducing the theoretical principles and
giving practical skills to use specialized software tools to extract
motifs from full-scaled NGS datasets (typically covering tens of Mb).


---------    Teachers    ----------

- Jacques van Helden, Aix-Marseille Université (France)
- Morgane Thomas-Chollier,  Ecole Normale Supérieure (France)
- Carl Herrmann, University Heidelberg (Germany).
- Alejandra Medina-Rivera, SickKids Research Institute, Toronto (Canada)

----------   Description   ----------

Next Generation Sequencing led to the development of novel methods
(ChIP-seq, FAIRE-seq, clip-seq, ) to acquire massive data about
diverse signals involved in genome regulation and function
(cis-regulation, chromatin conformation, RNA maturation,
recombination, replication, ...).

Extracting relevant information from the raw data requires not only
specialized software tools, but also a good understanding of their
principles and parameters.

In this tutorial we will demonstrate how to analyze ChIP-seq data
using the Regulatory Sequence Analysis Tools (RSAT,
http://www.rsat.eu/), via their different ways of access:
web-interface, command-line, and web-services.

This tutorial aims at introducing the theoretical principles and
giving practical skills to use specialized software tools to extract
motifs from full-scaled NGS datasets (typically covering tens of Mb).

----------    Contents    ----------

The tutorial will be organized in 2 half days:

1) Analysis of cis-regulatory elements with the Regulatory Sequence
Analysis Tools (RSAT): methods and website utilization
(http://www.rsat.eu/).

2) Using RSAT in command-line and via web services (SOAP/WSDL).

Topics:
- Motif discovery in NGS peak sets.
- Impact of the background models.
- Comparison between motifs.
- Motif enrichment in peak sequences.
- Evaluating the quality of motifs extracted from NGS peaks.
- Building control sets to estimate the rates of false positives.

----------   Topics not covered   ----------

Other steps for the analysis of ChIP-seq data (e.g. read mapping, peak
calling, functional enrichment of peaks, other tools for pattern
discovery and matching).

----------   Target audience   ----------

The course is addressed to bioinformaticians and biologists. The
afternoon will require being familiar with the Unix shell (Linux) and
basic programming skills (Perl or Python) to implement clients for web
services.

----------   In practice   ----------

* Participants will need to bring their own laptop.

* All command-line programs will be run on the IFB cloud platform
  (https://cloud.france-bioinformatique.fr/) managed by Christophe
  Blanchet (IBCP, Lyon, France). Each participant will be given a
  (free) account to access this cloud and thereby a fully functional
  virtual machine with RSAT.

* Wireless internet will be available at the conference venue.

* An indicative reading list will be available a few weeks before the
  tutorial.

* The hands-on will be organized in a cookbook mode: we will
  distribute protocols explaining the steps to solve selected test
  cases.

* For the practicals, we ensure that there is no need to transfer data
  from the conference room to the servers.

----------------------------------------------------------------