• 1. Introduction to Chipster

    In this section, you will learn how to use Chipster software, and where to find support and more information.

    Chipster is an easy-to-use graphical analysis software for high-throughput data such as RNA-seq and single cell RNA-seq. Chipster contains over 450 analysis tools and a collection of reference genomes. Chipster runs on your web-browser, while the actual analysis happens in the powerful cloud resources at CSC. 

    You don't need to know about command line usage, R or Python to get started, and any laptop with browser and decent internet connection will do. So to get started, all you need are credentials! If you are working, studying or otherwise affiliated to a Finnish university or research institute, you can log in to Chipster with your Haka or Virtu account, or request  CSC user account. If this is not the case, you can ask for a 3-week trial account. Chipster is also available as a free virtual machine image, and user accounts to CSC's server can also be bought. More info on accounts.


    First, watch the Chipster 101 video and check the Chipster quick tour below.

     

     

    You will need Chipster credentials to do the exercises. 

    You can log in to the web Chipster (Chipster v4) with your Haka or Virtu account, or with your CSC account. You can also request for 3 weeks evaluation account. 

    Next, please go through these exercises:

    1. Open Chipster: Go to https://chipster.csc.fi/, click on Launch Chipster (use the web-based Chipster version 4) and log in. 
    2. Open training sessionClick Sessions and select the session course_single_cell_RNAseq_Seurat under Training sessions.


    Finally, answer the quiz and question below.

Section 2