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<div>Hello</div>
<div>I have just started in this field of research and I want to annotate my assembled non-bilaterian invertebrate genome with Maker (100Mb in 7000 scaffolds) .</div>
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<div>I have red the maker tutorials but I am still a little uncertain about the iterative procedure. What I have already done is:</div>
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<div>- trained Augustus (using the web service) on the reference genome of a closely related species and its published dataset of "best transcripts" which are mainly based on gene prediction and some EST evidence. The published ESTs themselves were rejected from Augustus as being not sufficient for training (to few long transcripts).<br/>
- trained SNAP with the CEGMA-output of my genome<br/>
- assembled RNA-seq data with tophat/cufflinks and generated gff-file with cufflinks2gff<br/>
- de novo assembled RNA-seq data with Trinity</div>
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I have already done some preliminary Maker runs with initially trained Augustus, SNAP and some protein evidence which had good results.</div>
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<div>Now my strategy is:</div>
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<div>running maker with</div>
<div>- the est2genome option using the cufflinks gff and the Trinity transcripts as EST evidence</div>
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<div>- the protein2genome option using a protein file including all proteins of the closely related species, a less related non-bilaterian species and a collection of reviewed Swiss-Prot entries from one representative mammal and all protostomes</div>
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<div>- Augustus and SNAP for gene prediction</div>
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<div>When this is done I want to:</div>
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<div>- create 2nd training set for SNAP from the merged gffs with maker2zff<br/>
- train Augustus again with the Maker transcripts using the Augustus web service</div>
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And run Maker again</div>
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Is this a reasonable procedure? Or am I missing some important aspects here?</div>
<div>Thanks in advance?</div>
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