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How to select specific values (features and attributes) from gtf/gff file and convert it into table like data?

Generally gene information are reported in GTF/GFF format.

More details in these links: http://www.ensembl.org/info/website/upload/gff.html ,

http://mblab.wustl.edu/GTF22.html

But, there is often a need to mine the specific data (mainly features and attributes of these features) and represent in a more clear format which can be used with R, excel. How to do this?

gtf gff features attributes
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updated by h.mon h.mon • written by kirannbishwa01 kirannbishwa01

This seemed to me more a question with an answer from OP than a tutorial, so I edited the post.

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written by h.mon h.mon

1 answer

But, there is often a need to mine the specific data (mainly features and attributes of these features) and represent in a more clear format which can be used with R, excel. How to do this?

GTF_to_Table.py is a tool written on python3 which runs seamlessly for that purpose.

See the details on usage of this tools using the test_example files using this Github link: https://github.com/everestial/GTF_to_Table

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written by kirannbishwa01 kirannbishwa01

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