[maker-devel] About eAED

[Carson Holt]

eAED can be better for edge cases, but neither is perfect. Low AED generally correlates with better models. But a high AED does not mean the model doesn’t exist, it just means you should spend a little more time deciding if you really believe it or not.

—Carson


> On Oct 4, 2017, at 8:38 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> 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 <mailto: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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>> 
>> 
> 

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