Can I have different region cluster combinations?

This article is about how to analyse custom combinations of sequence region together. For more information about how clusters can be useful, see this article.

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
Heavy FR1
Light CDR1
Heavy CDR1
Light FR2
Heavy FR2
Light CDR2
Heavy CDR2
Light FR3
Heavy FR3
Light CDR3
Heavy CDR3
Light FR4
Heavy FR4
Light Constant Region
Heavy Constant Region
VDJ Region
VDJC Region
VJ Region
VJC Region
scFv Linker
scFv 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. 

Note that:

• 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.