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

[Matt Simenc]

Ah ok. A messy problem! I need to approximate strandedness for TE loci if
possible so will do some post processing using blast/hmmer to Repbase and
Dfam. Thanks for the speedy response Carson!

On Fri, Nov 17, 2017 at 6:23 PM, Carson Holt <carsonhh at gmail.com> wrote:

> 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
>
>
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