MAKER annotation post processing

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MAKER annotation post processing

Patrick Tran Van-2

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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Re: 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 <[hidden email]> 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

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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