[maker-devel] About eAED

[Quanwei Zhang]

Thanks for your explanation.

Best
Quanwei

2017-10-04 22:43 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> 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
>
> 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>:
>
>> 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
>> _______________________________________________
>> maker-devel mailing list
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>>
>>
>>
>
>
>
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