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- Click a Single cell counts data node
- Click the QA/QC section of the task menu
- Click Single cell QA/QC
By default, all samples are used to perform QA/QC. If there is more than one sample, you can choose to split the sample and perform QA/QC separately for each sample.
If your Single cell counts data node has been annotated with a gene/transcript annotation, the task will run without a task configuration dialog. However, if you imported a single cell counts matrix without specifying a gene/transcript annotation file, you will be prompted to choose the genome assembly and annotation file by the Single cell QA/QC configuration dialog (Figure 1). Note, it is still possible to run the task without specifying an annotation file. If you choose not to specify an annotation file, the detection of mitochondrial counts will not be possible.
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High-quality cells can be selected using the Selection card on the right, which is pre-loaded with three selection rules, one for each quality metric (Figure 5).
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