[maker-devel] About eAED

[Carson Holt]

The previous linked comment explains in detail —> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>

Basically the middle support of exon is inferred from edge support even though no overlap exists (so eAED infers support and AED does not).

—Carson


> On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> 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 <mailto: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 <mailto:xvazquezc at gmail.com>> wrote:
>> 
>> Carson commented on this here
>> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
>> 
>> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com <mailto: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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