[maker-devel] Maker v3.01 change-log + 3'UTR question

[Jason Stajich]

Luca - I would suggest PASA as a tool for 3'UTR (and 5'UTR) improvement in
gene annotation too. https://github.com/PASApipeline/PASApipeline

Funannotate has a step that can be use to run and update gene models if you
want to also take on from an existing maker run -
https://funannotate.readthedocs.io/en/latest/

Jason
Jason Stajich
jason.stajich at gmail.com


On Tue, May 19, 2020 at 1:33 AM Luca Peruzza <peruzzaluca at gmail.com> wrote:

> Hi There,
> I have two questions and I hope you guys can help me with them:
>
> 1. I have seen that maker version 3.01 is now out. Is there a change log
> available to see the changes in comparison to the previous maker version
> and have a glimpse of the new features of this release?
>
> 2. If I was to improve the annotation of my 3’ UTRs within a certain
> (non-model species) gff3, is there a particular way or a protocol to
> follow? I was thinking for example that Lexogen has released their 3’ UTR
> kit for RNA-seq of the three prime end of transcripts. Would it be possible
> to feed those reads to maker and somehow suggest that the reads are
> originating from the three-prime end so that this info is then passed in
> the gff3 file?
>
> Thanks a lot in advance for your help
> Best
> Luca
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at 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/20200519/2f7981e5/attachment-0004.html>