I am running CHiPseeker on differentially expressed peaks called by MACS2/DiffBind on ATAC-Seq data.

I had wrongly used hg19 on ChIPseeker but when I switched to hg38 I got the same list of genes at the same coordinates as hg19. To check I used IGV and found that all regions and genes called by ChIPseeker only matched when I was using hg19 in IGV.

Any suggestions on how to solve this issue?

I called the txdb object to make sure I had loaded hg38 and got confirmation:

TxDb object: 
Db type: TxDb Supporting package: GenomicFeatures Data source: UCSC # Genome: hg38 Creation time: 2023-09-20 17:25:17 +0000 (Wed, 20 Sep 2023)

Here are the commands I am running:

library(ChIPseeker) 

library(TxDb.Hsapiens.UCSC.hg38.knownGene) 

txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene 

seqlevels(atacV25.DB) <- paste0("chr", seqlevels(atacV25.DB))  

peakAnno <- annotatePeak(atacV25.DB, tssRegion = c(-3000, 3000), TxDb = txdb)