Tehdyt toimenpiteet

Workshop on next generation sequencing data analysis

Next generation sequencing (NGS) technologies deliver millions of short sequence reads for a relative low price. In addition to genome sequencing NGS has many genome-wide applications ranging from protein-DNA interaction studies (ChIP-seq) to transcriptome analysis (RNA-seq). This workshop covers NGS data analysis for genome assembly, ChIP-seq and RNA-seq. The workshop consists of a conference day and several hands-on days, and the participants can choose and combine the days that best suit for their research needs. The workshop is kindly sponsored by the EU FP6 Network of Excellence EMBRACE.

Program

31.5.2010

Hands-on: Analysing high-throughput sequencing data with Python and HTSeq

Teachers: Simon Anders (EMBL) and Nicolas Delhomme (EMBL)

There are many seemingly simple but cumbersome operations to adjust, filter, check, transform or otherwise preprocess read data before it can be given to an alignment tool, and likewise, custom post-processing is needed to analyse the alignment results. A scripting language like Python is very useful for this purpose, and the Python package HTSeq aims to make this as convenient as possible. We will explore HTSeq by programming simple scripts for common use cases. Some experience in programming (with Python or some other language) is expected. The material is available as html (updated) or as pdf.

____________________________________________________________

1.6.2010

Hands-on 1: Analysing RNA-Seq data

Teachers: Simon Anders (EMBL) and Nicolas Delhomme (EMBL)

Time: 9:30-14:15 (including lunch break)

In this hands-on session we will align example data from an RNA-Seq experiment against the genome, assign the reads to genes, count the expression of genes and then check for statistical significance of differential expression. For this purpose, we will use stand-alone tools (TopHat, htseq-count) and an R/Bioconductor package DESeq. Knowledge of R is useful but not necessary. For the material please see the vignette at the bottom of the DESeq page.

Hands-on 2: ChIP-seq data analysis and visualisation using Chipster

Teachers: Massimiliano Gentile (CSC) and Eija Korpelainen (CSC)

Time: 14:30-15:30

This hands-on session introduces how to analyse and visualise ChIP-seq data using the Chipster software, which provides a user-friendly graphical access to analysis tools. Chipster's versatile interactive genome browser enables the user to view mapped sequence reads and results in their genomic context. Material.

Hands-on 3: Visualising next-generation sequencing data with GenomeView

Teachers: Thomas Abeel (University of Gent/ MIT)

Time: 15:30-16:30

This hands-on session introduces how to visualise NGS data using GenomeView. GenomeView is a next-generation genome browser and annotation editor. Sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more can be displayed. Many file formats are supported for input and output. New functionality can be added using a plugin architecture. Material.

____________________________________________________________

2.6.2010

Conference: Next generation sequencing data analysis

Registration, coffee

9:30-9:35 Welcome by Eija Korpelainen (CSC)

Session 1: Assembly (chair: Eija Korpelainen)

9:35-10:20 Laurent Falquet (SIB): Experiences in assembling genomes with short reads data

10:20-10:40 Rainer Lehtonen (University of Helsinki): Sequencing and assembly of the Glanville fritillary butterfly genome

10:40-11:00 Panu Somervuo (University of Helsinki): Assembling the Glanville fritillary genome

Session 2: NGS data visualization and technologies (chair: Eija Korpelainen)

11:10-11:35 Thomas Abeel (University of Gent/ MIT): Visualising next-generation sequencing data with GenomeView

11:35-12:00 Asta Laiho (Turku Centre of Biotechnology): Living with SOLiD, Helicos (and Solexa)

Lunch

Session 3: ChIP-seq (chair: Simon Anders)

13:00-13:35 Teemu Kivioja (University of Helsinki, Karolinska Institut): Searching common target genes of oncogenic pathways from ChIP-seq data

13:35-14:00 Teemu Laajala (University of Turku): A practical comparison of methods for detecting TF binding sites in ChIP-seq experiments

14:00-14:20 Satu Nahkuri (University of Queensland): One exon, one nucleosome

14:20-14:40 Massimiliano Gentile (CSC): NGS data analysis and visualisation with Chipster

Coffee

Session 4: RNA-seq (chair: Thomas Abeel)

15:10-15:55 Simon Anders (EMBL): Differential expression analysis for sequence count data

15:55-16:30 Daniel Nicorici (FIMM): RNA-seq data analysis

_____________________________________________

3.-4.6.2010

Hands-on: Genome assembly

Teachers: Laurent Falquet (SIB) and Sandra Calderon (SIB)

This two-day hands-on session covers both de novo assembly and assembly by mapping onto a reference. Next generation sequencing data is frequently of low quality (noise and artifacts) and must be cleaned before usage. The assembly steps are often difficult due to the nature of the sequences (repeats and GC content). In this hands-on session you will learn how to measure the quality of the data, clean and extract the good information, perform the assembly, and evaluate the final results with various criteria.

-The first day consists of a lecture on assembly by mapping followed by exercises on quality control, mapping with with MAQ or Bowtie or BWA, and assessment and visualisation of the results. Slides.

-The second day consists of a lecture on de novo assembly followed by exercises on assembly with ABySS or SOAPdenovo or Velvet or Newbler, and assessment and visualisation of the results. Slides.

____________________________________________________________

Date: 31.05.2010 09:30 - 04.06.2010 16:30

Location: Premises of CSC at Keilaranta 14, Espoo, Finland (for how to find us, please click here). The hands-on days take place in the training room Dogmi, and the conference takes place in the auditorium. Each day starts at 9:30 and finishes at 16:30.

Language: English

Lecturers: As indicated above.

Price: 50 EUR per day

The fee covers course materials, lunches as well as morning and afternoon coffees

Registration

Registration has expired 17.05.2010 23:00

There are 24 seats for the hands-ons. Should there be more applicants, the participants will be selected based on their research interests indicated in the registration form. All the applicants will be informed about the participation by 20.5.2010. The registration can be canceled without a fee until 21.5.2010. Thereafter the full registration fee (50 euros/day) will be invoiced.

Additional information

For more information, please contact Eija Korpelainen (09-4572030, eija.korpelainen [at] csc.fi)

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More information

Tehdyt toimenpiteet

Workshop on next generation sequencing data analysis

Program

31.5.2010

Hands-on: Analysing high-throughput sequencing data with Python and HTSeq

1.6.2010

Hands-on 1: Analysing RNA-Seq data

Hands-on 2: ChIP-seq data analysis and visualisation using Chipster

Hands-on 3: Visualising next-generation sequencing data with GenomeView

2.6.2010

Conference: Next generation sequencing data analysis

_____________________________________________

3.-4.6.2010

Hands-on: Genome assembly

Registration

Additional information


Sisältö Course and event archive CSC's training facilities Training services More information about CSC customer training: courses at csc.fi. Follow us also on Twitter!	Tehdyt toimenpiteet Workshop on next generation sequencing data analysis Next generation sequencing (NGS) technologies deliver millions of short sequence reads for a relative low price. In addition to genome sequencing NGS has many genome-wide applications ranging from protein-DNA interaction studies (ChIP-seq) to transcriptome analysis (RNA-seq). This workshop covers NGS data analysis for genome assembly, ChIP-seq and RNA-seq. The workshop consists of a conference day and several hands-on days, and the participants can choose and combine the days that best suit for their research needs. The workshop is kindly sponsored by the EU FP6 Network of Excellence EMBRACE. Program 31.5.2010 Hands-on: Analysing high-throughput sequencing data with Python and HTSeq Teachers: Simon Anders (EMBL) and Nicolas Delhomme (EMBL) There are many seemingly simple but cumbersome operations to adjust, filter, check, transform or otherwise preprocess read data before it can be given to an alignment tool, and likewise, custom post-processing is needed to analyse the alignment results. A scripting language like Python is very useful for this purpose, and the Python package HTSeq aims to make this as convenient as possible. We will explore HTSeq by programming simple scripts for common use cases. Some experience in programming (with Python or some other language) is expected. The material is available as html (updated) or as pdf. ____________________________________________________________ 1.6.2010 Hands-on 1: Analysing RNA-Seq data Teachers: Simon Anders (EMBL) and Nicolas Delhomme (EMBL) Time: 9:30-14:15 (including lunch break) In this hands-on session we will align example data from an RNA-Seq experiment against the genome, assign the reads to genes, count the expression of genes and then check for statistical significance of differential expression. For this purpose, we will use stand-alone tools (TopHat, htseq-count) and an R/Bioconductor package DESeq. Knowledge of R is useful but not necessary. For the material please see the vignette at the bottom of the DESeq page. Hands-on 2: ChIP-seq data analysis and visualisation using Chipster Teachers: Massimiliano Gentile (CSC) and Eija Korpelainen (CSC) Time: 14:30-15:30 This hands-on session introduces how to analyse and visualise ChIP-seq data using the Chipster software, which provides a user-friendly graphical access to analysis tools. Chipster's versatile interactive genome browser enables the user to view mapped sequence reads and results in their genomic context. Material. Hands-on 3: Visualising next-generation sequencing data with GenomeView Teachers: Thomas Abeel (University of Gent/ MIT) Time: 15:30-16:30 This hands-on session introduces how to visualise NGS data using GenomeView. GenomeView is a next-generation genome browser and annotation editor. Sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more can be displayed. Many file formats are supported for input and output. New functionality can be added using a plugin architecture. Material. ____________________________________________________________ 2.6.2010 Conference: Next generation sequencing data analysis Registration, coffee 9:30-9:35 Welcome by Eija Korpelainen (CSC) Session 1: Assembly (chair: Eija Korpelainen) 9:35-10:20 Laurent Falquet (SIB): Experiences in assembling genomes with short reads data 10:20-10:40 Rainer Lehtonen (University of Helsinki): Sequencing and assembly of the Glanville fritillary butterfly genome 10:40-11:00 Panu Somervuo (University of Helsinki): Assembling the Glanville fritillary genome Session 2: NGS data visualization and technologies (chair: Eija Korpelainen) 11:10-11:35 Thomas Abeel (University of Gent/ MIT): Visualising next-generation sequencing data with GenomeView 11:35-12:00 Asta Laiho (Turku Centre of Biotechnology): Living with SOLiD, Helicos (and Solexa) Lunch Session 3: ChIP-seq (chair: Simon Anders) 13:00-13:35 Teemu Kivioja (University of Helsinki, Karolinska Institut): Searching common target genes of oncogenic pathways from ChIP-seq data 13:35-14:00 Teemu Laajala (University of Turku): A practical comparison of methods for detecting TF binding sites in ChIP-seq experiments 14:00-14:20 Satu Nahkuri (University of Queensland): One exon, one nucleosome 14:20-14:40 Massimiliano Gentile (CSC): NGS data analysis and visualisation with Chipster Coffee Session 4: RNA-seq (chair: Thomas Abeel) 15:10-15:55 Simon Anders (EMBL): Differential expression analysis for sequence count data 15:55-16:30 Daniel Nicorici (FIMM): RNA-seq data analysis _____________________________________________ 3.-4.6.2010 Hands-on: Genome assembly Teachers: Laurent Falquet (SIB) and Sandra Calderon (SIB) This two-day hands-on session covers both de novo assembly and assembly by mapping onto a reference. Next generation sequencing data is frequently of low quality (noise and artifacts) and must be cleaned before usage. The assembly steps are often difficult due to the nature of the sequences (repeats and GC content). In this hands-on session you will learn how to measure the quality of the data, clean and extract the good information, perform the assembly, and evaluate the final results with various criteria. -The first day consists of a lecture on assembly by mapping followed by exercises on quality control, mapping with with MAQ or Bowtie or BWA, and assessment and visualisation of the results. Slides. -The second day consists of a lecture on de novo assembly followed by exercises on assembly with ABySS or SOAPdenovo or Velvet or Newbler, and assessment and visualisation of the results. Slides. ____________________________________________________________ Date: 31.05.2010 09:30 - 04.06.2010 16:30 Location: Premises of CSC at Keilaranta 14, Espoo, Finland (for how to find us, please click here). The hands-on days take place in the training room Dogmi, and the conference takes place in the auditorium. Each day starts at 9:30 and finishes at 16:30. Language: English Lecturers: As indicated above. Price: 50 EUR per day The fee covers course materials, lunches as well as morning and afternoon coffees Registration Registration has expired 17.05.2010 23:00 There are 24 seats for the hands-ons. Should there be more applicants, the participants will be selected based on their research interests indicated in the registration form. All the applicants will be informed about the participation by 20.5.2010. The registration can be canceled without a fee until 21.5.2010. Thereafter the full registration fee (50 euros/day) will be invoiced. Additional information For more information, please contact Eija Korpelainen (09-4572030, eija.korpelainen [at] csc.fi)