Question: update a GFF file from an old assembly to a finished assembly
0
gravatar for thhaverk
5.3 years ago by
thhaverk0
Norway
thhaverk0 wrote:

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

 

 

methylation gff assembly software • 1.7k views
ADD COMMENTlink modified 5.3 years ago by Devon Ryan93k • written 5.3 years ago by thhaverk0
3
gravatar for Devon Ryan
5.3 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

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.

ADD COMMENTlink written 5.3 years ago by Devon Ryan93k

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

ADD REPLYlink written 5.3 years ago by thhaverk0
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