Some transcripts have no AED?

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Some transcripts have no AED?

wangzhennan

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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Re: Some transcripts have no AED?

Ence,daniel
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, "[hidden email]" <[hidden email]> 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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Fwd: Some transcripts have no AED?

Ence,daniel
In reply to this post by wangzhennan


Begin forwarded message:

From: "Ence,daniel" <[hidden email]>
Subject: Re: [maker-devel] Some transcripts have no AED?
Date: March 15, 2018 at 9:06:45 AM EDT
Cc: "Ence,daniel" <[hidden email]>

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, [hidden email] 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" <[hidden email]>
Sent Time:2018-03-14 19:33:01 (Wednesday)
To: "[hidden email]" <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
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, "[hidden email]" <[hidden email]> 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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Re: Some transcripts have no AED?

Carson Holt-2
In reply to this post by wangzhennan
Do they have no AED or an AED value of 0. A value of 0 means a perfect match to the evidence.

Also make sure you are not looking for AED in the predictions (i.e. GFF3 source column snap/augustus that are of type match/match_part). Those are rejected models and will not have quality statistics calculated for them (they are only there as alignments for reference purposes).

Only models with the source column of ‘maker’ and a type of 'gene/mRNA/exon/CDS’ represent the gene models and will have AED and QI values.

You can force MAKER to also calculate quality statistics for rejected models by altering pred_stats in the maker_opts.ctl file. 

pred_stats=0 #report AED and QI statistics for all predictions as well as models

—Carson

On Mar 13, 2018, at 9:53 PM, [hidden email] 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

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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