Question: GFF3 annotation filtering
0
gravatar for Ric
4 weeks ago by
Ric280
Australia
Ric280 wrote:

Hi, Is there a GFF3 annotation filtering tool:

  • which removes genes without a description and writes those in a different file
  • which removes gene names specific to user input and writes those in a different file?

Thank you in advance,

genome gene • 106 views
ADD COMMENTlink modified 4 weeks ago by Buffo1.7k • written 4 weeks ago by Ric280

Firstly, (as a side note ;) ) I would personally try to avoid adding gene description etc in a GFF file format. iI's not meant to hold that kind of info

Secondly, is the GFF file "complex"? if not then perhaps using linux commands such as awk or grep will get the job done?

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by lieven.sterck5.9k
1
gravatar for Buffo
4 weeks ago by
Buffo1.7k
Buffo1.7k wrote:

You can use GFFExaminer from Biopython.

ADD COMMENTlink written 4 weeks ago by Buffo1.7k
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