[maker-devel] annotation comparison

[Daniel Ence]

Hi Xiaofang, 

1. People use various ad-hoc scripts for comparing genome genome annotations. If you look in the MAKER2 paper(Holt and Yandell, BMC Bioinformatics 2011), you'll see the AED score, which is some we use to compare the support from the evidence. 

2.
It actually isn't surprising that you got that big of an increase in the number of genes when you turned "keep_preds" to 1. Ab-initio predictors give a great many false positives and "keep_preds=1" will turn all of those into gene models. 

To get more genes, you should probably train an additional gene predictor, like GeneMark and maybe augustus. I think that augustus should already have a config file for mosquito. 

Changing the "pred_flanks" will increase the number of genes if you think that you have many merged genes. 

What protein dataset did you use? We often use a set from a comprehensive protein database like uniprot in addition to proteins from closely related species. 

Thanks,
Daniel
Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of Xiaofang Jiang [jxf1023 at gmail.com]
Sent: Thursday, August 08, 2013 7:11 PM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] annotation comparison

Dear Maker Developers,

I am annotating a mosquitoes genome using Maker. I have two questions
regarding Maker annotation.

1. Are there any scripts available to compare two sets of annotations?
We know about SOBA but were wondering if there is something more
comprehensive that you guys use.

2. I am expecting around 13,000 genes, however maker only predicted
9,000 genes. I used both the gff3 from cufflinks, protein, and ESTs as
evidence and SNAP as the ab inito predictor. I changed "keep_preds" to 1
and that resulted 17,000 genes, it seems that shouldn't have happened.
So in order to get more genes, should I try change "single_length" to
100, and change "pred_flanks" to 100?


Best,

Xiaofang


_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org