[maker-devel] 99.98% of repeatmasker features on plus strand, anyone else seen this?

[Carson Holt]

While transposons that encode proteins will technically have a strand, simple repeats and many others do not so the algorithms used to find them will not necessarily assign a strand. For this reason the repeats are treated as strand-less since both strands are masked and are they are arbitrarily assigned to the plus strand to avoid issues with genome browsers that cannot handle strandless features.

—Carson



> On Nov 17, 2017, at 6:39 PM, Matt Simenc <mcsimenc at gmail.com> wrote:
> 
> Hi everybody,
> 
> I just noticed that the vast majority of features with type repeatmasker are on the plus strand in my MAKER GFFs. There are a handful on the minus strand. Has anyone else seen that in their MAKER GFFs?
> 
> MAKER 2.31.8
> 
> I looked at a standalone RepeatMasker run I did and the features are more evenly distributed between the +/- strands.
> 
> 
> Matt
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