Single Cell RNA-seq
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      How is Custom Cluster Annotation performed for Single Cell analysis?

      Cluster cells on specific genes of interest

      In order to annotate your Single Cell data with custom clustering, please follow these steps:

      1. Upload and run your Single Cell RNA-seq experiment first in ROSALIND without custom annotation
      2. Navigate to the Downloads folder in ROSALIND and download the desired 'Aggregate Samples' zipped file:
      3. Unzip the file 
      4. Open the Single Cell loupe file (.cloupe) with Loupe Browser (download from 10x Genomics website)
      5. Annotate clusters using Gene/Feature expression for your genes of interest and lasso tool (10x Genomics guidance here)
      6. Create Name for the clustering .csv file (for example: 'Custom Annotation') and name the clusters 
      7. Click the three dots next to the 'Custom Annotation' and select “Export Custom Annotation.” Choose to INCLUDE unlabeled cells. A .csv file will be generated.
      8. Then in ROSALIND, select “Design a New Experiment” then select the "10x Genomics" technology and "scRNA-seq Loupe Clustering" options
      9. Select the parent scRNA-seq experiment to apply the custom cluster annotation
      10. Upload the custom annotation .csv file