Dear all,

I forged a BSgenome with BSgenomeForge for the Indian medaka. This is what the seed file looks like:

Package: BSgenome.Omelastigma.NCBI.ASM292280v2

Title: Full genomic sequences for Oryzias melastigma (NCBI assembly ASM292280v2)

Description: Full genomic sequences for Oryzias melastigma as provided by NCBI (assembly ASM292280v2, assembly accession GCF_002922805.2). The sequences are stored in DNAString objects.

Version: 1.0.0

organism: Oryzias melastigma

common_name: Medaka

genome: ASM292280v2

provider: NCBI

release_date: 2020/04/13

source_url: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002922805.2

organism_biocview: Oryzias melastigma

BSgenomeObjname: Omelastigma

circ_seqs: "NC_018546.1"

SrcDataFiles: GCF_002922805.2_ASM292280v2_genomic.fna.gz from https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/30732/101/GCF_002922805.2_ASM292280v2

seqs_srcdir: /path/to/my/file/GCF_002922805.2

seqfile_name: genomic.2bit

However, when trying to use the forged package with Karyoploter package, I noticed that the assigned names are not the expected RefSeq (the ones I also have in my GTF file). an I have this "error" where I can clearly see that the names are something like "OmX":

NOTE: Not all requested chromosomes are part of the genome. Trying to filter as requested. Requested Chromosomes: NC_050512.1, NC_050513.1, NC_050514.1, NC_050515.1, NC_050516.1, NC_050517.1, NC_050518.1, NC_050519.1, NC_050520.1, NC_050521.1, NC_050522.1, NC_050523.1, NC_050524.1, NC_050525.1, NC_050526.1, NC_050527.1, NC_050528.1, NC_050529.1, NC_050530.1, NC_050531.1, NC_050532.1, NC_050533.1, NC_050534.1, NC_050535.1 Chromosomes in the genome: Om01, Om02, Om03, Om04, Om05, Om06, Om07, Om08, Om09, Om10, Om11, Om12, Om13, Om14, Om15, Om16, Om17, Om18, Om19, Om20, Om21, Om22, Om23, Om24, MT, etc...

Therefore, when I am trying to plot the DEGs at the chromosome level using Karyoploter I have a warning because, obviously, there is no matching between my created package and the names in the GTF file

Warning message: In .merge_two_Seqinfo_objects(x, y) : The 2 combined objects have no sequence levels in common. (Use suppressWarnings() to suppress this warning.)

and no plot.. Is there any way where I can reassign the names in my package or any other solution to be able to plot my DEGs at the chromosome level with Karyoploter?

Thank you!!