[maker-devel] control file for SNAP training

[Marc Tollis]

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> 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 <%28480%29%20965-7456>*
> marc.tollis at asu.edu
>
> *website: *https://sites.google.com/site/tollisresearch/
> *blog: *anolistollis.wordpress.com
>



-- 
*Marc Tollis, Ph.D.*
*Post-Doctoral Research Associate*
*Arizona State University*
*LSE 313*
*(480) 965-7456*
marc.tollis at asu.edu

*website: *https://sites.google.com/site/tollisresearch/
*blog: *anolistollis.wordpress.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150317/051bb315/attachment-0003.html>