[maker-devel] Prioritizing specific scaffolds to be annotated?

[Carson Holt]

There are many ways of doing this.  You can run everything separately and
then copy all GFF3 files into a common folder and use the gff3_merge script
that comes with maker to combine them.  Alternatively you can run maker with
the -g and -base options.  This allows you to specify a new genome on the
command line and the base name of the directory to write to.  Using those
flags you can swap in a different contig file while maintaining the same
output directory for your job as a whole.  Just run maker at the end of the
run using the original fasta and the -dsindex flag, to sync the datastore
index file so it is complete if you do this option.

To split out contigs of interest you can also use the fasta_tool that comes
with maker and use the -grep_header or ­select flags to indicate which
contigs to retrieve.

--Carson



From:  Bérénice Benayoun <benayoun at stanford.edu>
Date:  Wednesday, 21 November, 2012 1:45 PM
To:  <maker-devel at yandell-lab.org>
Cc:  Dario Riccardo Valenzano <dario1 at stanford.edu>
Subject:  [maker-devel] Prioritizing specific scaffolds to be annotated?

Hello,

I am using the pipeline to try and annotate the assembly of a genome that we
recently made in the lab (~70000 scaffolds).

We have a specific interest in selected contigs for biological reasons
(significant QTLs for a phenotype of interest that we'd like to link to
potential genes), though of course we want to annotate most of the genome in
the end.I was wondering if there was a way to bump some contigs up the list
?

I have tried to just extract the specific contigs into a smaller fasta file
and run maker separately just on them, but I don't know how to reintegrate
them in the final complete output in the end and if it's even possible.

Do you have any advice for this ?

Thank you so much in advance for your most invaluable help !

Sincerely yours,

Bérénice

-- 
Bérénice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
BRUNET Laboratory, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120 
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/ <http://www.stanford.edu/group/brunet/>
<http://www.stanford.edu/group/brunet/>
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20121121/ad8a5ea9/attachment-0003.html>