Question: GFF3 annotation filtering
0
gravatar for Ric
11 months ago by
Ric300
Australia
Ric300 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 • 273 views
ADD COMMENTlink modified 11 months ago by Buffo1.8k • written 11 months ago by Ric300

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 11 months ago • written 11 months ago by lieven.sterck8.2k
1
gravatar for Buffo
11 months ago by
Buffo1.8k
Buffo1.8k wrote:

You can use GFFExaminer from Biopython.

ADD COMMENTlink written 11 months ago by Buffo1.8k
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