You can specify arbitrary combinations of FR and/or CDR regions, and genes to cluster upon with the Antibody annotator.
Below is the default cluster combinations that are available whereby each line specifies a set of two or more genes and/or regions that should be clustered together:
Specifying arbitrary cluster combinations
To specify your preferred cluster combination of regions or genes, specify a cluster name followed by a colon followed by a comma separated list of genes or regions to combine. The genes and regions are available for clustering include:
Light V Gene
Heavy V Gene
Light D Gene
Heavy D Gene
Light J Gene
Heavy J Gene
Light C Gene
Heavy C Gene
Light Constant Region
Heavy Constant Region
To add the aforementioned syntax to the analysis, you will need to expand the Clustering Combinations text box by dragging the expand input box icon (denoted by the 2 diagonal lines on the bottom right edge of the text box). Once the text box is expanded, you can now input your cluster combination into the text box.
The following syntax is an example of how to cluster all the heavy CDR regions and this syntax is added to the Clustering Combinations text box:
Heavy CDR: Heavy CDR1, Heavy CDR2, Heavy CDR3
In this example, the cluster name is Heavy CDR and the regions that will be combined in this cluster are Heavy CDR1, CDR2 and CDR3.
- You can specify any name and any number of genes or regions to be combined but the genes and regions name to be combined are case sensitive.
- The default cluster combinations can be edited or removed and these default cluster combinations can be restored by clicking the Reset to default button on the bottom left of the NGS analysis popup.
Viewing specified cluster combinations
To view the clusters in your results, select you NGS result file, click the Sequences tab followed by Group by.
One you have selected your cluster combination in the Group by dropdown, the table will refresh and a column with your specified cluster combination will appear in the result table.
In this example, sequences that share identical heavy CDR1, CDR2 and CDR3 sequences are clustered together.