Filtering data to find samples

Overview

Once samples are uploaded into the CZ GEN EPI platform, you can easily find samples by filtering your data. Below are steps for filtering sample data to select for sequences of interest on the Sample page. Selected samples can then be easily navigated for downstream analyses or downloading data.

After reading this user guide, you will be able to filter samples by: 

• • Upload date
  • Collection date
  • Lineage
  • QC status

Filtering data

To filter samples by a given upload date, collection date, lineage of interest, and/or genome recovery status:

1. Go to workspace for the pathogen of interest and select filters from the the left-hand side menu of the Sample page.
   
   Filters are found on the left-hand side of the Sample page. You can select the filter of interest by clicking on the downward arrows.
2. Specify your desired data within selected filters. You can specify more than one filter for your data. For example, you can select for data representing a given lineage collected within a specified date range.
   
   Options within Upload Date, Collection Date, and Lineage filters.
   
   You can select from the following options for each filter:
   
   • Upload date: You can specify a date range (follow the indicated format for dates) or, for recently uploaded samples, you can specify samples uploaded the same (‘Today’), the day before (‘Yesterday’) or the last 7 days.
   • Collection date: You can specify a date range (follow the indicated format for dates) or number of days since the samples were collected based on preset intervals.
   • Lineage: You can specify one or more lineages of interest. You will be able to select from all the lineages represented in your samples.
   • QC status: You can specify if you only want to see samples with "Good" quality. 
3. See filtered samples on Sample page and keep track of set filters.
   
   Example of SARS-CoV-2 Sample page showing samples filtered by a single lineage.
4. If you want to see all the samples again on the Sample page, or remove a given filter, simply remove the filter(s) by clicking on the "X" within the purple rectangle highlighting each filter.

Filtering to search additional samples

You can select samples directly from your sample list and then use the filters to search and select additional samples. To do this:

1. Select sample(s) of interest from your sample list.
   
   Example of how you can use filters to search for additional samples after selecting samples from the Sample page. Keep track of the total number of selected samples by looking at the "Selected" number at the top right-hand side of the page. In this example, we are trying to find samples representing the BA.1.15 lineage after selecting one sequence representing the BA.1.1 lineage.
2. Set the appropriate filter to search for samples of interest and select additional samples.
   
   Example of how you can use filters to search for additional samples after selecting samples from the Sample page. In this example, we searched samples representing the BA.1.15 lineage after selecting one sequence representing the BA.1.1 lineage. After selecting five additional BA.1.15 samples, we have a total of 6 sequences selected for downstream analyses. You can continue directly with analyses or go back to the main sample list showing selected samples.
3. Continue with desired phylogenetic analyses or actions (editing metadata, downloading data, or deleting samples) for selected samples.