[maker-devel] Maker-derived CDS GFF3 phase column

[Rob Syme]

Fantastic. I thought that might have been the problem.

Looking forward to 2.28. Thanks!

Rob


On Wed, May 22, 2013 at 10:32 AM, Carson Holt <carsonhh at gmail.com> wrote:

> It looks like the phase was calculated from the wrong strand orientation.
>  I believe I have corrected this now.  I'm checking a few more things, but
> I'll have 2.28 as the latest release likely tomorrow with the cumulative
> bug fixes since the last release.
>
> Thanks,
> Carson
>
>
>
> From: Rob Syme <rob.syme at gmail.com>
> Date: Tuesday, 21 May, 2013 1:57 AM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Maker-derived CDS GFF3 phase column
>
> Hi all
>
> By my reading of the GFF3 spec (
> http://sequenceontology.org/resources/gff3.html), I'm getting gff3 from
> Maker that has odd data in the phase column.
>
> For example, see some example Maker output at
> https://gist.github.com/robsyme/5617399
>
> There are two exons, 5617 <- 5737 and 5793 <- 5953 with phases 0 and 2,
> respectively. Both exons are in the reverse strand.
>
> From the spec, phase indicates "the number of bases that should be removed
> from the beginning of this feature to reach the first base of the next
> codon", and for "reverse strand features, phase is counted from the end
> field".
>
> In the case of the 3' exon (5793 <- 5953), the end field (the 5th column)
> is 5953.
> The base at the end field is the first base of the translated CDS, so
> there should be no bases removed "to reach the first base of the next
> codon". I suggest that this phase should be 0, not 2.
>
> There is an illustration of the feature at http://i.imgur.com/DKLxnSf.png.
>
> The output gff3 is correct if "the number of bases that should be removed
> from the beginning of this feature to reach the first base of the next
> codon" is measured from the 'left-hand' end of this feature (the start
> field) rather than the end field.
>
> Has anybody else ran into this problem or am I misreading the gff3 spec?
>
> Rob Syme
> PhD Student
> Curtin University
>
>
>
>
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