[maker-devel] Reformat maker gff3

[Jenny Lee]

Hi all,

I would like to update my maker gff3 file to only contain the genes I've decided to keep - all maker genes, a subset of abinitio genes (which have interproscan hits). I would like to also exclude the repeats information and only retain the CDS, gene, exon and mRNA - like the format we usually see in published data.

I've been trying to do this manually and it gets messy. Any ideas?

Thanks a lot.

Regards,

Jenny Lee

[Xabier Vázquez Campos]

Can't you filter the file content with the 'grep' command? If you need to extract columns, use 'cut' too

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Xabier Vázquez-Campos, PhD
Research Associate
Water Research Centre
School of Civil and Environmental Engineering
The University of New South Wales
Sydney NSW 2052 AUSTRALIA

[Michael Campbell]

I’ve attached a protocols paper that walks through what you are trying to do. Let me know if it helps.

Mike