Analyses and Data Management

Analyses

In the Analyses tab, you'll see all the analyses in your study. The analyses will be displayed in card view by default. Each card will display the following information.

Information	Description
Analysis Name	Name of analysis.
Status	Status of analysis. See Analysis Statuses for a table of statuses and descriptions.
Analysis Type	Type of omic data used in the default or custom analysis.
Modified By	Last user who modified the analysis.
Date Modified	Date and time when the last update was made.

You can switch to list view by clicking the list icon in the top right. In the list view, you can customize the columns and filter your analyses. Click the info icon to get more detail about the analysis including error details.

Create Analysis

To create a new analysis, click .

Give your analysis a name and choose an analysis type from the dropdown menu.

Analysis Options

Analysis Option	Description
Default: Illumina Proteomics	General analysis pipeline for Illumina protein prep samples, with PCA and hierarchical clustering heatmap results. The maximum samples for analysis is 9,000.
Default: Illumina Single Cell Transcriptomics	General analysis pipeline for Illumina single cell prep samples, including the processing steps to output PCA and UMAP plots, plus graph-based clustering visualizations. For each sample, all features are reported and if feature ID's are not unique, Mean is used for Deduplication; raw counts are used as the count value format and cells with a total read count at least 400 are reported. The maximum samples for analysis is 1,000.
Default: Illumina Spatial Transcriptomics	General analysis pipeline for Illumina spatial samples, including a Spatial map with transcripts overlayed on the tissue image where each point is a grid. Graph-based clusters are also plotted on a UMAP and pie chart. The maximum samples for analysis is 100.
Default: Illumina Bulk Transcriptomics	General analysis pipeline for Illumina mRNA and Total RNA prep samples including PCA and hierarchical clustering heatmap results. The maximum samples for analysis is 500.
Default: Illumina miRNA	General analysis pipeline for Illumina miRNA prep samples including PCA and hierarchical clustering heatmap results. The maximum samples for analysis is 500.
Default: Illumina 5-base DNA Methylation	General analysis pipeline for 5-base DNA prep samples including regional methylation PCA plots, k-means clustering, and QC. The maximum samples for analysis is 200.
Custom: Multiomics	Available inputs include Illumina proteomics, single cell, spatial, and bulk transcriptomics, miRNA, 5-base DNA and Infinium methylation as well as third-party data types including Seurat (RNA), Seurat (ATAC), Somalogic ADAT, Gene counts in sf Format, and VCF. Two or more data types can be analyzed together in any combination.
Custom: Illumina Proteomics	Starts with the quantified samples which have undergone prior normalization and offers flexible analysis options. The maximum samples for analysis is 9,000.
Custom: Illumina Single Cell Transcriptomics	Starts with single cell counts and offers flexibility with the analyses pipeline step. For each sample, all features are reported and if feature ID's are not unique, Mean is used for Deduplication; raw counts are used as the count value format and cells with a total read count at least 400 are reported. The maximum samples for analysis is 1,000.
Custom: Illumina Spatial Transcriptomics	Two starting nodes as cell-binned or grid-binned data, including the spatial image outputs, and offers flexibility with the analyses parameters. The maximum samples for analysis is 100.
Custom: Illumina Bulk Transcriptomics	Starts with salmon format sample counts that have not been normalized and offers flexible analyses options. The assembly and annotation model used in secondary analysis is required to annotate the features. The maximum samples for analysis is 500.
Custom: Illumina miRNA	Starts with imported count matrix that have not been normalized and offers flexible analysis options. The maximum samples for analysis is 500.
Custom: Illumina 5-base DNA Methylation	Starts with importing selected 5-base methylation data and offers flexible analysis options. The maximum samples for analysis is 200.
Custom: Illumina Infinium Methylation	Starts with importing selected idat files and offers flexible analysis options.
Custom: Third-party analysis	Starts with data import. This option appears only when third-party assay data has been uploaded.

Next, select the sample, sample group, or all samples for the analysis.

If all samples are chosen for the analysis, a sample group will be automatically added to the Sample Groups menu containing all of the samples in the analysis.

Current spatial multisample analysis does not yet support the import of a mix of samples that use pipeline-manifest.json and samples that do not. When running an analysis on a sample group that has both types of samples, only those samples with a pipeline-manifest.json file will import.

Run Analysis

Click to run the analysis. You will receive a notification that the analysis was successfully created.

Wait for the analysis status to change from "Pending" to "Complete".

Analysis Statuses

The following table describes the different analysis statuses.

Status	Description
Pending	The analysis has been initiated but has not yet started. It is waiting in the queue to be processed.
In Progress	The analysis is currently being executed. The system is processing the data and generating results.
Complete	The analysis has finished, and the results are ready to be viewed. Click into the analysis to view it.
Error	The analysis has ended in error. Using the Analysis tab list view, click the info icon to get more information about the error type. The error can be further diagnosed using the Inspect analysis link.

Once the analysis is complete, you can click into it to view the results. Refer to the "Enter Analysis" section for more information on how to view your analysis.

Data

In the Data tab, you'll see a list of all the data and metadata files within your study from which your samples are derived.

Note that deleting data or metadata files will not remove any samples that were added to Connected Multiomics from those files. The samples will remain in Connected Multiomics even if the original files are deleted, ensuring that your sample data stays intact.