[maker-devel] MAKER annotation post processing

[Michael Campbell]

Hi Patrick,

For point 1, the best AED cutoff to use is quite arbitrary. For one the last genomes that I annotated we had a set of high quality genes identified based on synteny with genes in closely related genomes. We plotted the distribution of AEDs for those genes and found that a cutoff of 0.28 captured 98% of the high quality genes. This value would vary based on the evidence provided. I’ve used 0.5 in the past as a more permissive filter.

For point 2, these is a accessory script in the MAKER bin called quality_filter.pl. It has an option (-a) that allows you to put in an AED cutoff and it will filter the gff3 file based on that cutoff.

For general processing of GFF3 files, there is a perl library called GAL that is useful if you write code in perl.

Take care,
Mike

> On Jul 19, 2017, at 9:11 AM, Patrick Tran Van <Patrick.TranVan at unil.ch> wrote:
> 
> Hi,
> I have successfully annotated my genome with MAKER. Now I have a gff file that I want to post process /filter.
> 
> In particular, I would like to discard genes that are below to a certain AED score.
> 
> 1) Is there an AED treshold from where a gene is not strongly supported ? if yes, do you have some reference about this ?
> 
> 2) Is there a script/software to process a gff file ?
> 
> Thanks
> 
> 
> 
> Patrick Tran Van
> 
> Groups Chapuisat, Robinson-Rechavi & Schwander
> Department of Ecology and Evolution
> University of Lausanne
> Le Biophore
> CH-1015 Lausanne
> Switzerland
> Office 3206
> 
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