Excluding T cell receptor genes from Seurat object or integrated Seurat object?

[nilsrudqvist]

Hi all,

Thanks so much for creating Seurat for us to use.

I have several T cell 5' GEX libraries and a lot of my variable features and genes defining clusters are T cell receptor genes (TRB and TRA genes). For example:

I would like to remove TRB and TRA genes at some point, but not sure when. Should I remove these genes before integrating my libraries or can I exclude genes when calling variable features? I could not find this information when searching the forum nor using google.

Thanks in advance!
Nils

[prachi-sao]

Hello, did you determine what is optimal? Which is preferable, keeping TCRs or getting rid of them? What effect did this have on clustering?