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

[Bérénice Benayoun]

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/>
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