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Single cell genomics techniques have recently emerged as a powerful tool and already revolutionized the way we think about tissue heterogeneity, cell identity and gene regulation. We are at the beginning of a new era where these techniques are becoming standards and are universally applied for broad phenotyping and to answer biomedical questions. While this field is rapidly evolving and thriving driven by a core single cell omics community, the lack of expertise on these approaches hinders many Institutions and laboratories to take the leap. Despite the wealth of tools being developed, the toolset often become a jungle for the new comer: where should we start from? What is the best tool for the purpose? How can we be sure we are interpreting the results correctly? This EMBO Practical Course will empower researchers to use single cell technologies in their labs with confidence. It will teach the basics of single cell experimental and computational workflows guiding the participant from the tissue handling to the computational analysis. We will demonstrate the most common applications: single cell/nucleus RNA-seq and single cell ATAC-seq, with focus not only on the possibilities opened, but also on the bottlenecks, limitations and the strategies to overcome them.