Maker v3.01 change-log + 3'UTR question

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

Maker v3.01 change-log + 3'UTR question

Luca Peruzza-2
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
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: Maker v3.01 change-log + 3'UTR question

Jason Stajich-4
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
[hidden email]


On Tue, May 19, 2020 at 1:33 AM Luca Peruzza <[hidden email]> 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
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: Maker v3.01 change-log + 3'UTR question

Luca Peruzza-2
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 <[hidden email]> 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

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
[hidden email]


On Tue, May 19, 2020 at 1:33 AM Luca Peruzza <[hidden email]> 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
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org