New Tutorial: Single-cell ATAC-seq standard processing with SnapATAC2

Author(s) orcid logoTimon Schlegel avatar Timon Schlegel
new tutorial single-cell epigenetics

Posted on: 12 July 2024 PURL: https://gxy.io/GTN:N00094

We are proud to announce that a new training, explaining the analysis of single cell ATAC-seq data with SnapATAC2 and Scanpy, is now available in the Galaxy Training Network.

SnapATAC2 pipeline. Open image in new tab

Figure 1: SnapATAC2 standard processing pipeline. The single cell data is first preprocessed and a high-quality count matrix is produced. Next, the dimensionality of the data is reduced and clusters visualized. Finally, clusters are manually annotated with marker genes.

The tutorial consists of three sections: Preprocessing, Dimensionality Reduction and Clustering, and Cluster Annotation. During the preprocessing, cell-by-feature count matrices are created, which are filtered to produce high-quality AnnData count matrices. After that, the dimensionality of the data is reduced through nonlinear spectral embedding. The data is then projected onto two-dimensional space and clusters are identified. To annotate the clusters, the gene activity for each cell is measured and the activity of marker genes is visualized with the Scanpy package. The activity profile of each cluster is then used to determine the correct cell type.

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Analysis Pipeline with SnapATAC2

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