[maker-devel] About eAED

[Quanwei Zhang]

Thank you all.  Most time, the AED is equal to or lower than eAED, but
there are some genes whose eAED is smaller than AED. I feel the eAED is
more stringent than AED. Would you give me an example, under what condition
eAED can be smaller than AED?

The default maker2 gene set includes all genes with AED less than 1.  Do
you think eAED is a better choice to filter gene models than AED?

Best
Quanwei



2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> This one is an even better explanation than the answer I just gave. Thank
> you.
>
> —Carson
>
> On Oct 4, 2017, at 4:35 PM, Xabier Vázquez-Campos <xvazquezc at gmail.com>
> wrote:
>
> Carson commented on this here
> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ
>
> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>
>> Hello:
>>
>> I ran the maker2 pipeline and got the default gene sets (with AED<1). But
>> I found there are several hundred genes with eAED 1.
>>
>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can
>> be the reason of the great difference between AED and eAED. For this gene
>> it has a very low AED score, is it still a reliable gene model if its eAED
>> equals 1?
>>
>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
>> QI:75|0|0|1|0|0|2|111|35
>>
>> Thanks
>>
>> Best
>> Quanwei
>>
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>
>
> --
> Xabier Vázquez-Campos, *PhD*
> *Research Associate*
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
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