Pacific Analytics

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Cohorts ​

Cohorts allow you to discover and group sequencing data from public repositories for your own research. The platform is connected to major public data sources—most notably the NCBI Sequence Read Archive (SRA)—via our integrated Nexus database.

Building a Cohort ​

To start building a cohort, click the Build cohort button. This opens the Explore interface, where you can filter through millions of samples using various biological and technical metadata.

Dynamic Filtering ​

The Explore interface provides a faceted search experience categorized by Sequencing, Biology, Demographics, and more.

Filter Logic

Selecting filters across different categories (e.g., Library Strategy and Organism) uses AND logic. Selecting multiple values within a single category (e.g., two different Platforms) uses OR logic.

TIP

As you select filters, the counts for every other value across all categories are updated almost instantly. This allow you to see exactly how many samples are available for any combination of parameters before you even apply them.

The header of the interface provides a running total of matching samples, subjects, studies, and total files. Once you have refined your selection, click Save cohort.

Managing Cohorts ​

Once a cohort is saved, it appears in your Cohorts list. Selecting a specific cohort provides a detailed view of the associated metadata in a tabular format.

Data Import ​

Saved cohorts represent a metadata selection. To use the actual sequence data in your analysis, you must ingest the physical files:

  • Import files: Click Download Files to trigger the background transfer of FASTQ files from public archives (like ENA/SRA) to your project's storage.
  • Storage Tracking: The import dialog displays the total size of the requested files against the storage quota set by the system.

Cohort Actions ​

The cohort view includes several utility actions:

  • Analytics: Switch to the Analytics tab to view statistical distributions of the samples within your cohort.
  • Edit: Rename the cohort or add a description to provide context for your team.
  • Delete: Permanently remove the cohort selection from your project.

Need to define sample metadata for your workflows? Let's look at Sample Sheets! 📝