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null ChIP- and DNase-seq data analysis workshop
ChIP- and DNase-seq data analysis workshop
Date: 17.09.2014 10:00 - 20.09.2014 17:00
Location details: -
Language: english-language
lecturers: Several trainers as indicated in the program.
Price: -
Modern sequencing technologies enable efficient genome-wide investigation of regulatory regions. This international workshop covers several aspects of ChIP- and DNase-seq data analysis, ranging from quality control and alignment to peak calling, motif detection and annotation. The program consists of a lecture day and several hands-on modules that participants can choose from. This workshop is suitable for people with different backgrounds, ranging from biology to computer science, and for junior and senior researchers alike.

The workshop is kindly sponsored by the EU FP7 AllBio project, which aims to bring biologists and bioinformaticians together for the effective exploitation of high-throughput data. AllBio provides 15 travel bursaries of 500 euros for early stage researchers (PhD students or researchers with less than 8 years of experience after obtaining PhD).

 

AllBio logo

Program

Tuesday 16.9.2014

10:00-17:00 Hands-on module 1: "ChIP-seq data analysis with R/Bioconductor"
This practical tutorial covers peak calling, annotation, motif discovery and differential binding analysis of ChIP-seq data. The analysis tools used in the exercises include several R/Bioconductor packages such as chipseq, Biostrings, BSgenome, DESeq and Diffbind, so participants need to have experience in R programming.

Material

Trainers:

Borbala Mifsudi (UCL, UK)

Filipe Tavares-Cadete (Instituto de Biologia Experimental Tecnológica, Portugal)

 

Wednesday 17.9.2014

10:00-17:00 Hands-on module 2: "ChIP- and DNase-seq data analysis with Chipster"
This practical tutorial covers quality control, alignment, peak calling, annotation, motif discovery and genome browser visualization. The free, user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required, and the tutorial is thus suitable for everybody.

Trainers:

Eija Korpelainen (CSC): ChIP- and DNase-seq data analysis with Chipster: slides, exercises

Hashem Koohy (Babraham Institute, UK): Peak calling with MACS and F-seq

Jan Grau (Martin Luther University Halle-Wittenberg, Germany): Motif detection with Dimont: slides, exercises

 

Thursday 18.9.2014

10:00-15:00 Lectures
 

 

15:00-17:00 Hands-on module 3: "Using the computing resources of CSC in NGS data analysis"
This tutorial demonstrates how NGS analysis tools can be run using tens or hundreds of computing cores at CSC. In addition to the cluster environment, also  the cloud environment Pouta and the FGI grid are discussed. Basic knowledge of Unix is recommended for this session. This session is relevant for participants who have access to CSC's computing environment.
Material: slides, exercises

Trainer: Kimmo Mattila (CSC)

 

Friday 19.9.2014

9:00-14:00 Hands-on module 4: "ChIP-seq data analysis using command line tools"
This practical tutorial covers alignment, peak calling, annotation and motif discovery of ChIP-seq data. The analysis tools used in the exercises include several command line tools such as BWA, MACS, MEME and Homer, so participants need to be familiar with Unix.

Material: slides, exercises

Trainers:
Endre Barta (University of Debrecen, Hungary)
Gergely Nagy (University of Debrecen, Hungary)
 

 

14:00-17:00 Hands-on module 5: "DNase-seq data analysis using command line tools and introduction to pyDNase"
This practical tutorial covers peak calling with MACS and F-seq and detection of DNase-seq footprints. It also introduces pyDNase, a Python package for analysing DNase-seq data. Participants need to be familiar with Unix. For those that would like to do more bespoke analyses using the pyDNase library, Python experience is required.

Material for peak calling
Material for footprinting

Trainers:
Jason Piper (University of Warwick, UK)
Hashem Koohy (Babraham Institute, UK)