diff --git a/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.md b/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.md index 6e8980bb515cdc..0c3db57fed6f37 100644 --- a/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.md +++ b/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.md @@ -98,23 +98,26 @@ To start, let's get our dataset loaded into Galaxy. > {% snippet faqs/galaxy/datasets_import_via_link.md %} > > 3. **Rename** {% icon galaxy-pencil %} the datasets `Mito-counted AnnData` +> +> {% snippet faqs/galaxy/datasets_rename.md name="Mito-counted AnnData" %} +> > 4. Check that the datatype is `h5ad` > > {% snippet faqs/galaxy/datasets_change_datatype.md datatype="h5ad" %} > {: .hands_on} ->AnnData to Seurat ->If you have uploaded your data from Zenodo, and it came in AnnData format, we will need to convert this to a Seurat Object. This can be easily accomplished using the Seurat FilterCells tool. ->Simply run the tool without any actual filtering thresholds and with the following parameters: -> ->> Filter Cells ->> ->> Run{% tool [Seurat FilterCells](toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells/4.0.4+galaxy0) %} with the following parameters: ->> - *"Choose the format of the input"*: `AnnData` ->> - *"AnnData file"*: `Mito-counted AnnData` ->> - *"Choose the format of the output"*: `RDS with a Seurat object` -> {: .hands_on} -{: .tip} + +When you uploaded your data from Zenodo, it came in AnnData format, thus we will need to convert this to a Seurat Object. This can be easily accomplished using the Seurat FilterCells tool. +Simply run the tool without any actual filtering thresholds and with the following parameters: + +> Filter Cells +> +> Run{% tool [Seurat FilterCells](toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells/4.0.4+galaxy0) %} with the following parameters: +> - *"Choose the format of the input"*: `AnnData` +> - *"AnnData file"*: `Mito-counted AnnData` +> - *"Choose the format of the output"*: `RDS with a Seurat object` +{: .hands_on} + # Generating a Seurat object