Question: Comparing gff files
0
gravatar for guillaume.rbt
3.1 years ago by
guillaume.rbt620
France
guillaume.rbt620 wrote:

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!

sequence gene • 1.6k views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by guillaume.rbt620
1

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

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by 5heikki8.4k

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

ADD REPLYlink written 3.1 years ago by guillaume.rbt620
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