Combining annotations from multiple references

[stanleyjs]

Hi,

Is there support for aggregating annotations from multiple references?

For instance, we have some brain data that is not exactly the same region as the Allen human cortex you have provided. We also suspect the presence of endothelial cells and t cells. We would like to run the same query through multiple references (for instance multiple custom Allen references and a PBMC reference), collate the results, and then choose the "best match" from the multiple alignments. Is there a recommendation for how to achieve this or similar results?

[AustinHartman]

Hi, we don't currently provide an automated way to do this but the approach of mapping to two references and selecting the best cell type assignment for each cell seems reasonable. You could also try splitting your data up into multiple objects based on broad cell types. For instance, maybe one object contains only the cells you think are neurons and glial cells which you annotated with your custom brain references and the other object contains the predicted t cells which you annotate further with the PBMC reference