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<p>Hello,<br>
<br>
This is my first time running Maker for an insect genome annotation. <br>
<br>
I have found various resources and tried to make a consensus, I am looking for your thoughts and advices about my pipeline, if I can improve something or doing useless things:<br>
<br>
<br>
What I have:<br>
- RNA evidence: transcriptome<br>
- Proteine evidence: swissprot/uniprot + busco protein set of insect<br>
- Cegma and busco results of my genome<br>
<br>
<br>
1) Train SNAP with CEGMA<br>
<br>
2) Run (run A) maker with repeat masking with transcript, protein, the new SNAP file (from step 1) and augustus file (from busco).<br>
<br>
3) Create SNAP model from run A.<br>
<br>
4) Run (run B ) with the new SNAP (done at step 3) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_A.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1).<br>
<br>
5) Create SNAP model from run B.<br>
<br>
6) Run (run C) with the new SNAP (done at step 5) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_B.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1).<br>
<br>
7) Create SNAP model from run C AND Create Augustus gene model from run C<br>
<br>
8) Run (run D) with the new SNAP (done at step 7) + AUGUSTUS file (step 7) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_C.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1
and protein_pass=1). + Use keep_preds=1<br>
<br>
<br>
<br>
Does it seems coherent ?</p>
<p><br>
</p>
<p>Cheers,<br>
</p>
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<br>
Patrick Tran Van<br>
<br>
Groups Chapuisat, Robinson-Rechavi & Schwander<br>
Department of Ecology and Evolution<br>
University of Lausanne<br>
Le Biophore<br>
CH-1015 Lausanne<br>
Switzerland<br>
Office 3206<br>
<br>
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