[maker-devel] Repeatmasked genome

[Carson Holt]

Yes.  Those are all temporary files, that (if you still have them) you can
use to get at the masked fasta directly.  Otherwise you can just use the
features in the GFF3 file to remask the regions.

--Carson


From:  Daniel Ence <dence at genetics.utah.edu>
Date:  Monday, June 9, 2014 at 9:22 AM
To:  Marc Höppner <marc.hoeppner at imbim.uu.se>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Repeatmasked genome

Hi Marc, 

The masked genome sequence is stored in the "theVoid" directory for each
scaffold. There are files "query.fasta", "query.masked.fasta", and
"query.masked.gff". The masked sequence is in the query.masked.fasta file
and the genomic locations of the masked regions are stored in the
query.masked.gff. 

~Daniel



Daniel Ence
Graduate Student
dence at genetics.utah.edu
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

On Jun 9, 2014, at 2:48 AM, Marc Höppner <marc.hoeppner at imbim.uu.se>
 wrote:

> Hi,
> 
> this may be an odd question, but I was wondering where, if at all, Maker
> reports the repeat-masked genome sequence? As far as I can tell the fasta
> sequences included in the gff annotation are unmasked (?) or at least not
> softmasked. I guess it wouldn’t be too hard to take the repeat masker features
> and use them to soft mask the assembly, but still...
> 
> Regards,
> 
> Marc
> 
> 
> Marc P. Hoeppner, PhD
> 
> Department for Medical Biochemistry and Microbiology
> Uppsala University, Sweden
> marc.hoeppner at imbim.uu.se
> 
> 
> 
> 
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