[maker-devel] annotation comparison

[Xiaofang Jiang]

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