How to concurrently filter RNA and CITEseq data within seurat object

Question

[cook.675]

I have a Seurat object I created from RNA and CITEseq data. I load the matrices and create a seurat object with assays for each ("RNA" and "ADT"). The dimensions are identical as are the column barcodes.

I want to filter the data based on counts/feature counts/%MT (so, from the RNA side) and subset the matrix with my filter, but have the cells removed from both the RNA and the ADT data set simultaneously.

When I run: Object <- subset(Object, subset = nCount_RNA > 1050 & nFeature_RNA > 300 or similar, the resulting matrix has the ADT assay deleted. I assume this is because I'm telling it to subset with only the RNA data, but its not clear to me how to remove the same cells from each assay at the same time?

Answer 1

[cook.675]

Hey guys this is solved! I used a function to trim the antibody names before I did the QC step and it was causing this problem for some reason