[maker-devel] about predictor training

[熹熹]

Hi,

I'm trying to use MAKER to annotate the new genome sequence which I assembled by myseft. I used TopHat and Cufflinks to align the sequence based on the RNA-seq we have. Based on the tutorial of MAKER, I may need three fasta format file including assembly data, ESTs and protein database to train the SNAP. I may use SwissProt as the protein database. Can I use the gtf result from Cufflinks directly as an ESTs during the training? 
Another is, if I want to use Augustus to do the ab initio gene prediction, do I need to do the same way as SNAP? Cause I saw some posts that the result from ab initio would be used as the evidence to train the predictor. Can I ask is there has some order doing the prediction in different predictor?

Thank you so much for you help.

Lin
 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130512/0a2f1f5b/attachment-0002.html>