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

[Carson Holt]

Also MAKER clusters overlapping repeats to generate the best masking of the assembly. For the GFF3 it then assigns the name of the repeat encompassing the greatest portion of the cluster to the feature (i.e. the best representative). But the cluster is technically build from overlapping repeats on both strands (repeats tend to jump on top of other repeats, so they stack with bits and pieces of other repeats at the edges). Yet another reason why everything is just assigned to the plus strand.

—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
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org