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 samples and custom analysis, respectively. Note that this does require at least an Illumina Connected Multiomics (ICM) Professional subscription in order to create a custom analysis.

Add Data

After navigating to the corresponding study, select +Add Data. (Note: Illumina Connected Analytics (ICA) is now Illumina BioInsight Platform Core (Platform Core); ICM may continue to show ICA naming during this transition.) For this example, select Select from ICA project.

Select OTHER DATA TYPES: Single-cell > scRNA feature-barcode-matrix.

Following this selection, a description page is displayed for review of the supported file formats before selecting Select format.

After selecting the format, the following screen will display the content of the linked Platform Core Project. Navigate to the corresponding Single Cell Analysis containing the features, barcode, and matrix files.

For example, 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 unfiltered 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 the Samples tab, select the corresponding sample (for the generic sample, it should have the suffix .scRNA or .scRNA.filtered), and select + Create analysis. Provide an Analysis name, then proceed with Analysis Type - Custom.

Select Run Analysis, then the following screen will display 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 [e-mail].