[maker-devel] annotation comparison

[Li, Michael]

I'd be interested in knowing about this too. I'm writing an internship work report on this topic, so it would be great to hear about it.

I personally use ParsEval to compare two sets of annotation. It seems pretty thorough, but it's still in its early stages of development. You can read a bit more about it here: https://github.com/standage/AEGeAn

Cheers,
Michael 

-----Original Message-----
From: maker-devel [mailto:maker-devel-bounces at yandell-lab.org] On Behalf Of Xiaofang Jiang
Sent: Thursday, August 08, 2013 9:12 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


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