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!!
And just to give you a complete picture, I am trying to perform the following tutorial: https://bernatgel.github.io/karyoploter_tutorial//Examples/GeneExpression/GeneExpression.html adding the columns with the differential expression results to my created GRange object as metadata columns (mcols) so I'll have an annotated GRanges. I made the txdb with:
and then I used the genes function to create a GRanges object with all genes