Importing raw Single Cell RNA Data into Illumina Connected Multiomics

Illumina’s built-in pipelines allow for auto-ingestion of multiomics data to reduce the amount of customer inputs. If more flexibility of the input files is desired, the samples and analysis can be set up as generic sample and custom analysis, respectively. Note that this does require at least an ICM Professional subscription in order to create a custom analysis.

Add Data

After navigating to the corresponding study, select the Samples tab, select +Add Data.

Select Single Cell > sc-RNA

Following the selection, select scRNA feature-barcode-matrix, then Select format.

The following screen will display the content of the linked ICA Project. Navigate to the corresponding Single Cell Analysis containing the features, barcode, and matrix files.

Select the corresponding files

• .features.tsv.gz

• .barcodes.tsv.gz

• .matrix.mtx.gz

  

Note: If importing DRAGEN Single Cell RNA analysis, two sets of files will be present. The “filtered” files will contain only the cells that pass the corresponding thresholds used, and the number of cells will match the “Passing Cells” metric of the DRAGEN Report. If manual filtering is desired, the un-filtered files can be imported, and the ICM Task “Cell Barcode QA/QC” can be used to draw a barcode rank plot and manually select the desired filtering level.

Once the corresponding files are selected, select Add selected data to your study in the bottom right corner of the page.

+ New Analysis

From the Studies UI, select +New Analysis.

Provide an Analysis name, then select Analysis Type - Custom: Third Party Assays. Then select the corresponding sample (for the generic sample, it should have the suffix .scRNA). Once selecting, the Assay File Format will auto populate to scRNA feature-barcode-matrix.

Select Run Analysis.

A new analysis will be created that will immediately go to Status - Pending. After which, the refresh button can be selected to update the status and will show Needs Input.

Select the Analysis, and it will update the screen to the File format options.

The settings here can be updated, and if desired, the Report cells with total read count at least can be changed or disabled completely.

After the desired settings have been selected, select Finish to initiate the Import process.

For any feedback or questions regarding this article (Illumina Knowledge Article #10024), contact Illumina Technical Support [email protected].