[maker-devel] Reformat maker gff3

[Michael Campbell]

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

> On May 12, 2016, at 8:37 PM, Xabier Vázquez Campos <xvazquezc at gmail.com> wrote:
> 
> Can't you filter the file content with the 'grep' command? If you need to extract columns, use 'cut' too
> 
> On 13 April 2016 at 13:05, Jenny Lee <h.lee12 at uq.edu.au <mailto:h.lee12 at uq.edu.au>> wrote:
> 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
> 
> 
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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
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