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null Next generation sequencing data analysis with Chipster
Next generation sequencing data analysis with Chipster
Date: 14.06.2012 9:00 - 16.06.2012 17:00
Location details: -
Language: english-language
lecturers: Eija Korpelainen
Massimiliano Gentile
Ilari Scheinin
Jarno Tuimala
Kimmo Mattila
Price: -
This course covers several aspects of NGS data analysis and visualization, ranging from quality control, filtering and alignment to more specific tasks such as finding differentially expressed genes and detecting copy number aberrations, variants, methylation and ChIP-seq peaks. The course consists of lectures and hands-on exercises. As the user-friendly Chipster software is used for the exercises, no prior knowledge of NGS data analysis or unix is required.

This course is kindly sponsored by the SeqAhead COST Action, which provides travel bursaries of 650 euros for 15 participants. If you would like to apply for a travel bursary, please fill in the corresponding section in the registration form. Everybody who comes from the European union area and has no more than 8 years of research experience after obtaining PhD (COST definition for early stage researchers) can apply for a travel bursary. The course is kindly sponsored also by the Biomedinfra project, which provides a service cloud for Chipster.


Chipster integrates a comprehensive collection of analysis tools for high-throughput data such as NGS, microarrays and proteomics. For details regarding the NGS functionality, please see NGS tool content. Chipster also contains a built-in genome browser, allowing users to view reads and results in their genomic context. Users can save their analysis pipelines as reusable automatic workflows, and both workflows and analysis sessions can be shared with colleagues. Chipster software is open source and the server installation package is freely available.

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Program

The course starts every day at 10 am and finishes at 5 pm

Wednesday 13.6.2012

  • Introduction to Chipster
  • Quality control and filtering reads (FastQC, FastX, PRINSEQ)
  • Alignment to reference genome (Bowtie, BWA, TopHat)
  • Manipulation of BAM files (SAMtools)
  • Visualization of aligned reads in their genomic context (Chipster genome browser)
  • Matching genomic regions (BEDtools, HTSeq)

Thursday 14.6.2012

  • ChIP-seq: Peak detection (MACS), retrieving nearby genes and performing pathway analysis for them
  • RNA-seq: Finding differentially expressed genes (Cufflinks)
  • miRNA-seq: Finding differentially expressed miRNAs (edgeR, DESeq)

Friday 15.6.2012

  • Basic variant calling (SAMtools)
  • CNA-seq: Calling copy number aberrations
  • Methyl-seq: Methylation analysis (MEDIPS)

 

Course data

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Day 3