Background models help to filter out contamination, noise, and microorganisms whose presence is expected in the report page and heatmap. Metagenomic next-generation sequencing is very sensitive and can easily pick up microbes present in the lab environment rather than the original sample. Furthermore, biological tissues can contain genetic material from common benign microorganisms that a user may wish to filter out when looking for disease agents. Creating a set of healthy or clean samples that act as the control can help identify unusual pathogens.
To create a new background model navigate to the My Data section of IDseq. You can either navigate into a project or select the Sample tab to see all of your IDseq samples.
To start building your background model select the samples you would like to include using the blue check-mark to the left of the sample name.
Filter samples if you only want to select a subset. If you want to discover infecting agents you should create a background model with water controls and known infection-negative samples of the same tissue type.
The total number of selected samples will be visible above the table in the right-hand corner.
Click on the hard drive icon when you are happy with your selection.
A dialogue will pop up with options to name and describe your background model.
Review your selected samples and click Create.
Click out of the modal when you are done to return to your project screen. If your background model includes a large number of samples it may take a few minutes to generate.
Once background generation is complete, you can use your background on the heatmap and the single sample report.
When looking at a single sample you can select your new background from the background dropdown filter.
Select the new background model to update the Z score and the aggregate score in the table.
When looking at the heatmap you also have an option to select the background model. If you want to view the Z score on the heatmap you can change the Metric selection to be NT or NR Z score. The heatmap will update automatically.