[maker-devel] Maker annotation of large scaffolds

[Seth Munholland]

I would think splitting could work if you generate a sufficient overlap.
IE 1-100k, 50-150k, etc.  Reassembling the annotations for the overlap
regions may be tricky if you get conflicting annotations though.

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

On Thu, Jun 22, 2017 at 2:39 AM, Aravind PRASAD <aravindp at imcb.a-star.edu.sg
> wrote:

> Hi All,
>
>
>
> I’m trying to annotate a fish genome using Maker pipeline. It could finish
> the annotation for maximum scaffolds except 5 of them which are of size
> around 100M base pairs. The current clusters in our institute has a time
> limit of 24hrs for a job and these scaffolds could not be annotated with in
> that time.
>
> Can you please suggest any other way of finishing the annotation for large
> scaffolds?
>
>
>
> I thought of chunking up the scaffolds to run, but, I’m afraid that would
> split a gene into two.
>
> Thanks for your time.
>
>
>
> Regards,
>
> *Aravind PRASAD <aravindp at imcb.a-star.edu.sg> :: Research Officer ::
> Comparative and Medical Genomics Lab :: Institue of Molecular and Cell
> Biology (IMCB) :: Agency for Science, Technology and Research (A*STAR)*
>
> 61 Biopolis Drive :: #5-04 Proteos :: Singapore 138673:: DID (+65) 6586
> 9573 <+65%206586%209573> :: Fax (+65) 6779 1117 <+65%206779%201117> ::
> http://www.imcb.a-star.edu.sg/
>
>
>
> [image: 2]
>
>
>
>
>
>
> Note: This message may contain confidential information. If this Email/Fax
> has been sent to you by mistake, please notify the sender and delete it
> immediately. Thank you.
>
> _______________________________________________
> 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/20170622/9e829c28/attachment-0003.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image002.png
Type: image/png
Size: 18240 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20170622/9e829c28/attachment-0003.png>