[maker-devel] control file for SNAP training

[Carson Holt]

You can also add additional protein file if you want more evidence than that already in the GFF3. It makes re-annotation and adding evidence to an already annotated genome file really easy.

—Carson


> On Mar 17, 2015, at 3:26 PM, Marc Tollis <mtollis at asu.edu> wrote:
> 
> I answered my own question:
> No need to re-align proteins again - takes too long.
> So, I used the gff file from the gff_merge on the log file from the first run (the one with just protein2genome). Then, after generating the .hmm file, I put it in my control file, along with protein2genome=0, removed the protein.fasta, set maker_gff and protein_pass=1. The output now shows that only snap is running, and no blastx and exonerate - a relief because it is much faster!
> 
> On Sun, Mar 15, 2015 at 7:19 AM, Marc Tollis <mtollis at asu.edu <mailto:mtollis at asu.edu>> wrote:
> This is a question about process, and to make sure I am doing things right (when time is of the essence, some mistakes can set you back weeks).
> 
> I have run maker on my de novo vertebrate genome, using only the predictive proteome from a congener (well-studied and available on Ensembl), and generated the HMM for the first round of SNAP training. As per the 2014 tutorial, I edited the control file for this step as follows: I added the path to the .hmm file, and set protein2genome to 0. 
> 
> When I run maker, I notice that in addition to snap, it is still running blastx and exonerate however. I noticed that this is because I did not remove (or "comment out") the path to the protein.fa in the control file (the output looks markedly different when I do comment out the protein file - and I can't even tell if it's running snap in this instance). 
> 
> Is it simply using exonerate to place the ab initio predictions on the scaffolds (meaning that having protein2genome=1 is to tell maker to make evidence annotations) ? Did I do this correctly, or should I also remove the protein.fa out of the control file for SNAP training? 
> ​
> -- 
> Marc Tollis, Ph.D.
> Post-Doctoral Research Associate
> Arizona State University
> LSE 313
> (480) 965-7456 <tel:%28480%29%20965-7456>
> marc.tollis at asu.edu <mailto:marc.tollis at asu.edu>
> 
> website: https://sites.google.com/site/tollisresearch/ <https://sites.google.com/site/tollisresearch/>
> blog: anolistollis.wordpress.com <http://anolistollis.wordpress.com/>
> 
> 
> -- 
> Marc Tollis, Ph.D.
> Post-Doctoral Research Associate
> Arizona State University
> LSE 313
> (480) 965-7456
> marc.tollis at asu.edu <mailto:marc.tollis at asu.edu>
> 
> website: https://sites.google.com/site/tollisresearch/ <https://sites.google.com/site/tollisresearch/>
> blog: anolistollis.wordpress.com <http://anolistollis.wordpress.com/>_______________________________________________
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