Exon Editor Window

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Exon Editor Window

Alexandre Beaudoin

​​My users are currently still using the first version of Apollo (the Java Web Start one), but it does not run with any reasonably new version of Java.  They regularly use the "Exon Editor" window to make changes to models and search for short sequences.


I do not see anything equivalent to the Exon Editor window in the Apollo2 interface, and the Blat search does not seem to return any results for short nucleotide sequences (under 30) *could you return a warning when the sequence is too short?*


Am I missing anything? do you know what tools people use to modify gene models (not just promote/demote existing models)?


Thanks,

  Alexandre Beaudoin


Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada





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Re: Exon Editor Window

nathandunn




On Oct 1, 2018, at 6:45 AM, Alexandre Beaudoin <[hidden email]> wrote:

​​My users are currently still using the first version of Apollo (the Java Web Start one), but it does not run with any reasonably new version of Java.  They regularly use the "Exon Editor" window to make changes to models and search for short sequences.

I do not see anything equivalent to the Exon Editor window in the Apollo2 interface,

Most things should be there.  Especially structural edits.  

Have you gone through the user’s guide: http://genomearchitect.github.io/users-guide/ ? 


and the Blat search does not seem to return any results for short nucleotide sequences (under 30) *could you return a warning when the sequence is too short?*

I was able to do a BLAT search with under 30 nucleotides.   However, maybe  the same BLAT code is returning an error that isn’t being bubbled up? 

You can also do a File -> Add Sequence Search track for something similar.  However, I would see if you can’t get the BLAT tool working.  

Do you have any log files associated with it? 

Am I missing anything? do you know what tools people use to modify gene models (not just promote/demote existing models)? 

You should be able to right-click or simply drag from the evidence area to the yellow annotation area.  

In addition to the user’s guide, I’m unsure if this presentation will help or not: https://www.slideshare.net/nathandunneugene/apollo-bosc2018

Feel free to ask more questions or open GitHub issues:  https://github.com/GMOD/Apollo/issues

Cheers,

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory
[hidden email]

Thanks,
  Alexandre Beaudoin

Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada



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