This is my first post here.
My problem is the following.
I have a GFF file with the locations of DNA methylation sites for a bacterial genome coming from the pacbio. This was the GFF file based on the assembly provide by the sequencing lab. Since the genome assembly was not closed, I put work into closing that genome assembly, and that is now done.
However, this rearranged all the positions of the methylated sites, so I would like to liftover my GFF file to the finished genome assembly. So far I have only found tools that use genomes from Human, mouse or other model organisms, such as CrossMap or liftover on Galaxy.
Is there anybody that knows how I can do this correctly?