[maker-devel] Fwd: Some transcripts have no AED?

[Ence,daniel]

Begin forwarded message:

From: "Ence,daniel" <d.ence at ufl.edu<mailto:d.ence at ufl.edu>>
Subject: Re: [maker-devel] Some transcripts have no AED?
Date: March 15, 2018 at 9:06:45 AM EDT
To: "wangzhennan at ioz.ac.cn<mailto:wangzhennan at ioz.ac.cn>" <wangzhennan at ioz.ac.cn<mailto:wangzhennan at ioz.ac.cn>>
Cc: "Ence,daniel" <d.ence at ufl.edu<mailto:d.ence at ufl.edu>>

Hi, I really can’t help you without more information to answer either of your questions (number of genes or the transcripts without AEDs). If you ran maker with some evidence to annotation those 23000 genes, then some of those genes were probably not supported by the evidence. Did you give those 23000 genes as predictions or as models? Those are two different options in maker and would give different results.

~Daniel



On Mar 15, 2018, at 4:11 AM, wangzhennan at ioz.ac.cn<mailto:wangzhennan at ioz.ac.cn> wrote:


Hi,

   I am so sorry that I can not expound my question for you. I run maker with a annotation file(gff) which has 23000 genes, but I got a result with only 21553 genes. Why there were fewer genes than original file? Thank you very much!

   Best wishes.


                                                                                                                                                                               Wang



-----Original Messages-----
From:"Ence,daniel" <d.ence at ufl.edu<mailto:d.ence at ufl.edu>>
Sent Time:2018-03-14 19:33:01 (Wednesday)
To: "wangzhennan at ioz.ac.cn<mailto:wangzhennan at ioz.ac.cn>" <wangzhennan at ioz.ac.cn<mailto:wangzhennan at ioz.ac.cn>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Some transcripts have no AED?

Hi, can you send a few lines of examples? Do some transcripts do have AEDs?

~Daniel

Sent from my iPhone

On Mar 13, 2018, at 23:54, "wangzhennan at ioz.ac.cn<mailto:wangzhennan at ioz.ac.cn>" <wangzhennan at ioz.ac.cn<mailto:wangzhennan at ioz.ac.cn>> wrote:


Hi,

   When I used maker to get the AED value, some transcripts have no AED values in the result. Why? I used the RNA-Seq data and protein to run maker.Thank you.

   Best wishes.


                                                                                                                                                               Wang

T

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