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bioinformatics tool for RNA-seq data analysis: ideas wanted

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  • bioinformatics tool for RNA-seq data analysis: ideas wanted

    Hi all

    I'm planning to design a software tool for a bioinformatics programming project at university. It is mostly for fun during summer, but better if the software is useful and reusable for community, it would be more motivating. I have no restriction on software type, it can be anything. I mostly know python and bash, and not used to more low-level languages such as C++ or Java. A cute and useful script is what I am aiming at.

    I have direct access to NGS RNA-seq data for D. melanogaster whole body females:
    - Illumina HiSeq2500 paired-end reads (.fastq)
    - Oxford MinION (.fast5, can be extracted to .fastq as well)

    So, what would you suggest? Maybe, something related to isoform detection/benchamarking going besides the standard pipelines?

    Thank you in advance for your ideas.

  • #2
    Use the illumina reads to generate ideal electrical sequence models, then try to match those models quickly to the MinION reads (event model, or raw signal).

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