I've just created a new GFF off a new version of a genome X using liftOver tool. I would like to know any method to verify the content stored in this new GFF. I mean, I'm looking for a way to compare the old GFF information with the new gFF one. For example:
- See if the genes have changed.
- See if the coordinates of a old transcript have changed (due to indels in my new genome). Check that the new coordinates correspond actually with the old transcript (same fasta sequence).
I'm thinking about extracting transcript sequences from both GFF (old and new), and blast them against each other to see the length of the alignment, see the differences between both versions...etc.
If anyone has done this kind of analysis (or if anyone has any idea about this), I would like to hear new opinions/suggestions.
P.S: I don't want to validate the GFF format, I want to check the information (content) of the new annotation in comparison to the old one.