With the CosmosID app you can easily manage and view all of your samples. If needed you can create folders and move relevant samples into them to keep them organized. When you click on the folder icon on the left panel you will see all of your folders and samples.
From main dashboard, click on a sample name.
You will see sample information and various controls across the top and a table with microbial results.
The top navigation bar provides information about your sample, allows you to navigate between different databases and filtered vs unfiltered results, and allows you to change taxonomy levels when viewing results.
To see how many organisms or genes (depending on the database being viewed) were identified for your sample, look at the number found, as circled above.
The number of taxonomically significant hits that were found in your sample and used to make identifications are listed as a number followed by "HIT".
The total number of reads in your sample is listed as well.
Click the drop down menu to select the database results to view:
- Antibiotic Resistance
- Dark Matter (Beta)
- Respiratory Virus
- Virulence Factors
** Filtered vs Total Results
You are able to view both filtered and unfiltered (total) results for your sample. Filtered results contain the calls that have met the threshold for high confidence that the organism called is in the sample. Unfiltered results contain additional calls that are below the filtering threshold and may need further validation to determine if they are truly present in the sample.
You would typically use filtered results when you are looking at data where you want high confidence in your calls, like when working with clinical data. Many people use unfiltered (total) results when looking at environmental samples where there may be organisms whose genomes are more novel or diverge from most reference genomes.
The filtering threshold which determines if results are considered significant is based on internal statistical scores determined by analyzing a large number of diverse metagenomes. Organisms listed in the filtered results are likely to be present in the sample. Unfiltered (total) results include those in the filtered results and usually additional organisms. Organisms listed in the unfiltered (total) results but not in the filtered results need further validation to determine if they are actually present in the sample - either by deeper sequencing of the sample followed by re-analysis or by orthogonal validation using targeted PCR or other methods.
The taxonomy switcher button allows you to select the taxonomic level results to view for both the sample dashboard table and the sample visualizations.
To view strain level results click “Strain” on the taxonomy switcher at the top of the window. The dashboard table view provides a strain level report.
You can download your results as tab-separated files (which can be opened in Excel) or as PDFs. Click on "Export" and select the type of file you would like to download. Download should begin immediately. To download visualizations, navigate to the one of interest and click Export.
Updated 6 months ago