Questions pertaining to useSeqnames function

[sylestiel]

Hi@rcorces,

With reference to the section 1.5.2 Using Non-standard Genomes in ArchR the manual mentions, " if your seqnames are just integers, you will need to supply them as characters i.e. useSeqnames = c("1", "2", "3") instead of useSeqnames = c(1, 2, 3)."

I would like to know the following:
1)Where do we incorporate this line of code (that is useSeqnames)?
2)Do we have to make sure that the genomeAnnotation and geneAnnotation steps do not introduce the chr prefix as well and if so how can that be accomplished?

My libraries of interest are as follows:
library(BSgenome.Mmulatta.UCSC.rheMac10)
library(TxDb.Mmulatta.UCSC.rheMac10.refGene)
library(org.Mmu.eg.db)

Thanks!