Chipster training courses

We run several training courses on different aspects of bioinformatics every year in Finland and abroad. The courses at CSC are open for everybody, but you can also contact us to discuss options for hosting a course on your site.

We make our course materials publicly available so that anyone can download them for their own use. The materials include slides and exercises, and many courses have also lecture videos. The exercise data are available as example sessions on the Chipster server, and we also provide ready-made analysis sessions which you can use as a reference when doing exercises on your own. We can also provide training accounts to our Chipster server in Finland.

We run currently the following Chipster courses (follow the links for more info). CSC runs also other bioinformatics courses, you can find the upcoming courses in our course calendar.

  1. RNA-seq data analysis
  2. Single cell RNA-seq data analysis
  3. Virus detection using small RNA-seq
  4. Community analysis of amplicon sequencing data (16S)
  5. Detection and annotation of genomic variants
  6. ChIP-seq data analysis
  7. Microarray data analysis

RNA-seq data analysis

This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The course takes two days (or one long day if you omit exercise sheets 3 and 4). You will learn how to Course material (2017):

Single cell RNA-seq data analysis

This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. Both DropSeq and 10X Genomics data are used in the exercises. The course takes one day. You will learn how to Course material (2018):

Virus detection using small RNA-seq

This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences. The course takes about 5 hours. You will learn how to Course material (2018):

Community analysis of amplicon sequencing data (16S)

This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The course takes one day. You will learn how to Course material (2017):

Detection and annotation of genomic variants

This course covers variant analysis from raw sequence reads to variant annotation, introducing the theory, analysis tools and file formats involved. The course takes one day. You will learn how to Course material (2016):

ChIP-seq data analysis

This course covers ChIP-seq analysis from quality control and alignment to peak calling, motif detection, and pathway analysis. It introduces the theory, analysis tools and file formats involved. The course takes one day. You will learn how to Course material (2016):

Microarray data analysis

This course covers microarray data analysis from quality control and normalization to differential expression analysis, clustering and pathway analysis. It introduces the theory, analysis tools and file formats involved. The course takes one and half day. You will learn how to Course material (2016):