My problem is the following, I have some bed files whose genomic regions are annotated using the chromosome (chr__ start end ... ...), and I want to use the ncbi gff3 to extract the info but this file is annotated using accession.version numbers. Bedtools oblige me to use the same location nomencaluture thus I need to transform the accession to chr base.
So far I know that the number of the "NC_" prefixed accessions id specify the chromosme, (i.e: NC_000001.11: chr1, NC_000002.12: chr2, ..., NC_000023.11: chrX, NC_000024.10:chrY, NC_012920.1: chrM ). Nevertheless, how can I know which is the chromosome of the accessions prefixed with NW_ or NT_?
Some "NT_ , NW_" are alternative assemblies of NC_ and the info contained is "the same" being placed lines below that NC_, but some others do not and contains genes of interest which I could be loosing when using bedtools i.e https://www.ncbi.nlm.nih.gov/gene/3806. Some do not have a known location but that gene is known to be in the chromosome 19 and I can not deduce it from its accession number.
Is there a way of getting the chromosome from the accession number? Or shall I extract the info from another annotation file?