Isoform quantification plugin development

Serhat Gueler

• September 20, 2016 08:57

Hi,

We would like to develop a plug-in that does isoform quantification. We will basically use our isoform quantification tool (Mix-Square) running as a command line in the background. Before starting with the implementation of the plug-in I'd like to get your opinions about the design and the feasibility of the project.

What our tool needs is a BAM and a GTF/GFF file; therefore, I need to export the alignments in BAM file format as well as the annotations in GTF/GFF format. The results (expression values/read counts) are stored just in a simple tsv file. The expression values then need to be imported back into the Geneious and converted to known object format. Do you foresee any restrictions that may come up during the development of our pug-in ?

Thank you,
Serhat

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  Richard Moir

  • September 29, 2016 22:52

  Thanks for getting in touch, It's great to hear you are considering plugin development.

  Geneious does have importers and exporters for both BAM and GFF3 which you can call programmatically from your plugin. The main challenge I can see for you will be around importing the results.

  Firstly you cannot export GFF on an alignment, you will have to call it on the reference sequence stand alone.

  Secondly, I would recommend including the reference sequence inside the GFF file or as a FASTA file that is imported into Geneious at the same time as the new GFF expression data. Attaching calculated expression levels to the original data is not really possible via the API right now without a fair amount of work.

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  Serhat Gueler

  • October 25, 2016 14:34

  Thanks for your reply Richard. I will discuss it with my team and then we will decide whether we will continue with development of the plug-in or not.
  
  Best.

  Serhat

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