QA/QC & Data Processing

Once the data has been imported in the project we can start pre-processing the data:

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• We can now normalise our filtered data. Click Normalization and scaling > Normalisation. Use the recommended settings by clicking :

Data Exploration

Now that we have filtered low quality cells and normalised our data, we can start clustering to identify cell populations.

• Click on the normalised data node, then from the menu on the right select Exploratory analysis > PCA. We are going to use the top 2000 features by variance and calculate the first 50 principal components (PCs):

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• Once the PCA has run, click on the resultant node and select Exploratory analysis > UMAP. Run the UMAP as default:

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• While the UMAP is running we can also queue a clustering analysis. Select Exploratory analysis > Graph-based clustering. We are going to use the Leiden algorithm to cluster our data. In the advanced settings, set the resolution parameter to 1e-4 and click Apply:

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