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Old 06-20-2016, 06:42 AM   #1
Location: Russia

Join Date: Jul 2014
Posts: 18
Default 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.
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Old 06-21-2016, 08:31 AM   #2
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 835

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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bioinfomatics, illumina, ngs, rna-seq, software

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