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

[Valerie Soza]

Hi Carson

Thanks, that is simple and it worked.

I did the following to sort and concatenate the query.masked.fasta files into one fasta:

$ find Rwill7.maker.output -name 'query.masked.fasta' | sort -t "/" -k 5 | xargs cat > Rwill7.maker.assembly_masked.sorted.fasta

-Valerie

> On Mar 15, 2018, at 8:31 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> 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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> 

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/