Next-Generation Sequencing Workshop

Premises of CSC at Keilaranta 14, Espoo, Finland.

Premises of CSC at Keilaranta 14, Espoo, Finland.

This course covers several aspects of next generation sequencing (NGS) data analysis and visualization, ranging from general tasks such as quality control, alignment and genomic region matching to the more specific tasks such as peak detection (ChIP-seq) and finding differentially expressed genes (RNA-seq). 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 primarily targeted for researchers who already have NGS data, or who are planning to start such experiments soon.
Chipster integrates a comprehensive collection of analysis tools for high-throughput data such as microarrays, proteomics and NGS. For NGS data there is currently functionality for ChIP-seq, RNA-seq, miRNA-seq, methyl-seq and CNA-seq data (for details, please see NGS tool content). Users can save their analysis pipelines as reusable automatic workflows, and both workflows and analysis sessions can be shared with colleagues. Access to CSC's Chipster server is free of charge for Finnish universities.


Thursday April 26, 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)

Friday April 27, 2012

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