Comparing gff files

Question

[guillaume.rbt]

Hi everyone,

I'm currently trying to compare several gff annotation files from the same species, and I would like to get common genes between the annotations (same start/stop, exon/intron positions). Would anyone knew a tool that does this kind of comparison?

Thanks!

[5heikki]

Same 'start/stop, exon/intron positions' assumes that all the files are adjusted to begin from the same nucleotide. This is often/usually not the case. For pairwise comparisons, you can parse relevant fields to new files and use man comm

[guillaume.rbt]

Thanks for your response, Indeed annotation data are often heterogeneous... I will probably parse my files as you advised in the end.