[maker-devel] Repeatmasked genome

[Daniel Ence]

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<mailto: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<mailto: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<mailto:marc.hoeppner at imbim.uu.se>




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