Single cell ATAC-Seq possible?

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1

Is it possible to perform single cell ATAC-seq on Galaxy? Are there any plans to have this going forward?

Thanks!

2

Hi,
There is currently Episcanpy available on Galaxy for scATAC-seq data analysis. There is a scATAC-seq preprocessing tutorial available on GTN. After this tutorial, you can use a scRNA-seq analysis workflow for clustering. Alternatively, you can follow the analysis vignettes from EpiScanpy because all the required functions are available on Galaxy. The underlying data type is anndata. You can also switch between Scanpy tools and EpisScanpy.
Best,
Pavan

1 Like
3

Much appreciated for the update!

Cheers