Question

Post about extracting information from GFF

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20 months ago

yoser4 ▴ 10

hello everyone I want to get some "clean comments" from the GFF file. Is there any software or code that can do this? Any help will be appreciated.

GFF • 1.0k views

ADD COMMENT • link updated 20 months ago by GenoMax 147k • written 20 months ago by yoser4 ▴ 10

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ADD REPLY • link 20 months ago by yoser4 ▴ 10

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This is what my current GFF file looks like

ADD REPLY • link 20 months ago by yoser4 ▴ 10

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What is clean comments?

ADD REPLY • link 20 months ago by GenoMax 147k

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I updated the format I want below. Do you have any ideas?

ADD REPLY • link 20 months ago by yoser4 ▴ 10

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enter image description here

ADD REPLY • link 20 months ago by yoser4 ▴ 10

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This is what I want. The key point is that the annotation information in the last column is more "concise"

ADD REPLY • link 20 months ago by yoser4 ▴ 10

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You can list the attributes from the last column and remove what you don't need with AGAT. ID and Parent are mandatory and has to be kept.

ADD REPLY • link 20 months ago by Juke34 8.9k

score 0 · Answer 1 · 2023-03-16

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20 months ago

GenoMax 147k

Anything related to GTF/GFF try looking at AGAT toolkit: https://agat.readthedocs.io/en/latest/?badge=latest

ADD COMMENT • link 20 months ago by GenoMax 147k