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satijalab / azimuth

A Shiny web app for mapping datasets using Seurat v4
https://satijalab.org/azimuth
GNU General Public License v3.0
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RunAzimuth not working with SCT assay #203

Closed anoop1988 closed 8 months ago

anoop1988 commented 8 months ago

Hi, when I run RunAzimuth() using seurat object with default assay "SCT" (I did SCTransfrom the object prior to Azimuth) the process running into error as below,

HIV_No_Doublet <- RunAzimuth(HIV_No_Doublet, reference = "pbmcref",assay = "SCT")
error below,
Finding anchors
Error in indices.ba[neighbors.ab, 1:k.anchor, drop = FALSE] : 
  subscript out of bounds

But it is running properly a if I change the default assay "RNA". So Azimuth will not work with SCTransformed data?

Gesmira commented 8 months ago

Hi, Azimuth does the preprocessing on the raw query data directly. It uses the SCTransform internally, thus you should not use the "SCT" assay. By default, we use the "RNA" assay to get the raw counts and then they will be SCTransformed as part of the preprocessing.