This article outlines how to add cluster(s) to a Biologics Annotator Result. When adding clusters, the Graphs tab will be updated to show the relevant added cluster graphs, and any new clusters will be viewable in the Cluster Table dropdown. This is different from taking a subset of sequences and reclustering the subset, described here: Subsetting sequences and re-calculating Clusters.
If you are unsure what a cluster is and why they are useful, see Understanding "Clusters".
How to Add Cluster(s)
To add a cluster to a result, navigate to any Biologics Annotator Result Document and go to Post-processing > Add Clusters (Recluster)
This should bring up the Add Clusters pop-up, where you can click the blue + icon to bring up the cluster creator widget:
Here you can add simple clusters using the Quick Select tab, or switch to the Advanced tab to add inexact (percentage based) or multi-region clusters. A more in-depth explanation of this can be found here: Clustering Options.
Below is an example showing a generic Clonotype-like cluster, where sequences will be grouped according to an 85% match across the Heavy CDR3 while the V Gene and J Gene must be the same.
If you would like to learn more about clonotypes, see Understanding Clonotypes or watch the video below.
Viewing the results
Once the Add Clusters job has completed your Biologics Annotator Result document should be updated with the specified clusters***
*** Please note that the All Sequences table is not updated after Add Cluster is run. This means that any new added clusters (eg. VDJ Region (97% Identity) in the image below) will not have a corresponding column in the All Sequences table.
Following Add Clusters, the following should be available in your annotation result:
- Re-calculated clusters accessible via the Cluster Table dropdown menu
- New relevant graphs added to the graphs tab