[maker-devel] RepeatMasker masking olfactory receptors

[Aurelie K]

Hi Annabel,

I would run RM by specifying your (group of) species, using the -s option
of Repeat Masker, mostly if you have a custom de novo library. This will
limit the cross masking of repeats that have been identified in other
species.

Cheers,
Aurelie

On 30 March 2017 at 11:51, Annabel Beichman <annabel.beichman at gmail.com>
wrote:

> Hi Carson,
> I have a question about RepeatMasker within Maker —
> I am finding that all class II olfactory receptors (families like OR2,
> OR5) are being masked by RepeatMasker as “RTE-BovB” repeats. This leads to
> them not being annotated by Maker. I don’t expect my species (a mustelid)
> to have a large number of Bov-B repeats, and when I put the sequences
> annotated in my genome as RTE-BovB into repbase’s CENSOR only 13 out of 960
> sequences have a hit to anything in repbase. If I put those same sequences
> into NCBI blast, however, they all blast to olfactory receptors. I am
> finding the same pattern with another related mustelid de novo genome, and
> took the Ensembl ferret genome and ran it through the same pipeline and am
> finding a large number of Bov-B repeats there as well, despite there being
> none in the official annotation of that genome.
>
> I used RepeatMasker with all species libraries, plus a custom library from
> RepeatModeler.
>
> Any idea what might be going on?
>
> Thanks so much!
>
> ~ Annabel
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20170330/97f3d84b/attachment-0003.html>