immunoglobulin genes

[NoemieL]

Hi,

I am looking at immune cells that are sequenced in both scATACseq and scRNAseq from the same samples.

In the scRNAseq data using Seurat, we have a lot of immunoglobulin genes that are not present in the scATACseq data using ArchR
Do you have any idea why? Is there a way to get them in the ArchRProject?

Exemple of genes find in scRNAseq data
grep(pattern = "^(IG[KHL])", x = rownames(x = MM.merge@assays$RNA@counts), value = TRUE)
[1] "IGKC" "IGKV4-1" "IGKV3-7" "IGKV1-8" "IGKV1D-8" "IGHEP2" "IGHMBP2" "IGHA2" "IGHG4"
[10] "IGHG2" "IGHGP" "IGHA1" "IGHG1" "IGHG3" "IGHD" "IGHM" "IGHV3-21" "IGHV3-23"
[19] "IGHV1-24" "IGHV4-59" "IGHV3-64" "IGLVI-70" "IGLV6-57" "IGLV11-55" "IGLV1-51" "IGLV1-50" "IGLV9-49"

The only genes find using the getMatrixFromProject(ArchRProj ,useMatrix = "GeneScoreMatrix") and converted in Seurat project in order to use scGate. (error when using scGate: The following genes were not found IGKC,IGHG3,IGHG1,IGHA1)
grep(pattern = "^(IG[KHL])", x = rownames(x = ATAC_data_seurat@assays$originalexp@counts), value = TRUE)
[1] "IGHMBP2" "IGLON5" "IGLL5" "IGLL1"

Thanks

[rcorces]

ArchR doesnt dictate which genes are included. This is dictated by your geneAnnotation. If you are using a default geneAnnotation then this is dictated by the corresponding BSGenome object. The only way around this is to forge your own BSGenome object.