[maker-devel] augustus exon calling ~

[Salim Bougouffa]

Hi,

I should have mentioned a third scenario where an exon is not called fully
by maker despite augustus getting it right (figure artemis03)

[image: artemis03.png]


On Sun, 21 May 2017 at 10:48 Salim Bougouffa <mjfi2sb3 at gmail.com> wrote:

> Hi Maker folks,
>
> I have several issues with a plant genome annotation that I am currently
> doing but perhaps the most recurrent issues are:
>
> 1/ CDSs that are missed where significant rna-seq evidence is there
> (figure artemis01)
> 2/ vice versa where one or two exons are added without rna-seq
> evidence/intron hints (figure artemis02)
>
> info about the runs:
> 1/ using augustus with a pre-existing model for a related plant that has
> high homology to the one I am annotating
> 2/ umask=1 (seems to do better than umask=0; is this a good thing to do)
> 3/ evm = 1 (seems to perform better than emv=0)
> 4/ repeatmasking (denovo + repbase)
>
> Best,
> /SB
>
>
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