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

[Luca Peruzza]

Thanks Jason,
Yes, my idea was to add extra 3’UTR info to an existing maker gff3 file. If you say that funannotate can do it, I’ll have a look.

Thanks
Luca

> On 20 May 2020, at 01:29, Jason Stajich <jason.stajich at gmail.com> wrote:
> 
> Luca - I would suggest PASA as a tool for 3'UTR (and 5'UTR) improvement in gene annotation too. https://github.com/PASApipeline/PASApipeline <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/ <https://funannotate.readthedocs.io/en/latest/>
> 
> Jason
> Jason Stajich
> jason.stajich at gmail.com <mailto:jason.stajich at gmail.com>
> 
> 
> On Tue, May 19, 2020 at 1:33 AM Luca Peruzza <peruzzaluca at gmail.com <mailto: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
> 
> 
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