Landmark Registration Advice
Manually checking landmark registration can be time consuming, but it’s a useful way to ensure effective ADT integration. One tricky step of landmark registration is setting effective marker_bandwidth values to maximize on automatic peak detection. In our experience with multiple CITE-seq panels (TotalSeq A, B, and C), the best marker_bandwidth value for individual antibodies are consistent across panels. Thus, to help jumpstart the process, below is a list of some of our modifications to marker_bandwidth for various antibodies. For markers not listed, the built-in default (0.2) seems to work consistently.
We hope to continue to update this page, expanding advice to additional antibody panels and sample types! If you have any input, click here, and create a “New issue” button, choose “Submit advice”.
Bandwidths for human immune cell markers
(Applies to the Universal TotalSeq-A, B, and C panels)
Marker Name |
marker_bandwidth |
|---|---|
CD2 |
0.1 |
CD3 |
0.1 |
CD7 |
0.1 |
CD16 |
0.15 |
CD19 |
0.15 |
CD28 |
0.5 |
CD32 |
0.15 |
CD35 |
0.175 |
CD40 |
0.5 |
CD56 (NCAM) |
0.15 |
CD62L |
0.1 |
CD82 |
0.3 |
CD94 |
0.15 |
CD107a (LAMP-1) |
0.5 |
CD123 |
0.6 |
CD127 (IL-7Ra) |
0.15 |
CD163 |
0.15 |
CD185 (CXCR5) |
0.3 |
CD335 (NKp46) |
0.15 |
Ig light chain k |
0.3 |