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 ?
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