something about genome reference

[jefferyUstc]

Hi， I got a question about BSgenome.Hsapiens.UCSC.hg38 and EnsDb.Hsapiens.v86, from internet, i get to know that both two are annotations of hg38, one is UCSC hg38, another is ensemble hg38. my peaks were called by ucsc hg38. So， what if i run with below codes:

annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86)
seqlevelsStyle(annotations) <- 'UCSC'
genome(annotations) <- "hg38"
Annotation(seurat_obj) <- annotations

is that inappropriate ?

[timoast]

If your data was mapped to hg38 (UCSC-style genome), then you need to supply gene annotations in the same style, so it makes sense to change the seqlevelStyle here to UCSC for the gene annotations.