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

[Carson Holt]

You will just have to find and concatenate the files yourself.

Something like —> find assembly.maker.output -name 'query.masked.fasta' | xargs cat > assembly_masked.fasta

—Carson


> On Mar 7, 2018, at 2:19 PM, Valerie Soza <vsoza at uw.edu> wrote:
> 
> 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/
> 
> 
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