update a GFF file from an old assembly to a finished assembly

Question

[thhaverk]

Hi,

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?

Thomas

Answer 1

[Devon Ryan]

Have a look at the LiftOver Howto page from UCSC for instructions on how to create your own liftOver files. You can then just use liftOver.

[thhaverk]

Thanks. I had missed that it was possible to create your own liftOver files. Will try it.