[maker-devel] how to output masked genome from MAKER

[Valerie Soza]

Hi MAKER community

I am wondering whether it is possible to get the entire masked genome generated by MAKER as an output. I think I have found it in pieces in the query.masked.fasta files generated for each scaffold by MAKER in theVoid directories. Is there a script that anyone has used to collate these files?

I am aware of the fast_merge script that comes bundled with MAKER, but it does not seem to collate the query.masked.fasta files. Could this perl script be modified to do this action? 

Thanks for any help or insights.

-Valerie

Valerie Soza, Ph.D.
c/o Hall Lab
Department of Biology
University of Washington
Johnson Hall 202A
Box 351800
Seattle, WA 98195-1800
206-543-6740
http://staff.washington.edu/vsoza/