[maker-devel] Repbase subscription

[Carson Holt]

Yes. Do a manual install of RepeatMasker with HMMER as the aligner and Dfam as the reepeat database (free). Run RepeatModeler to get an assembly specific repeat dataset and give that to MAKER. The combination of the two will allow you to mask sufficiently for the annotation.  If for any reason you want to classify the repeats into families for further analysis rather than just mask them out, then you want a RepBase subscription.

—Carson


> On Feb 2, 2022, at 10:05 AM, Taslim, Cenny <Cenny.Taslim at nationwidechildrens.org> wrote:
> 
> Hi,
>  
> I just have a quick question before spending time to install maker. Now that Repbase requires active subscription as of April 2019, it is possible to run maker without Repbase?
>  
> Thanks,
> Cenny
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/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/20220202/44b81086/attachment-0003.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20220202/44b81086/attachment-0003.p7s>