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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). -
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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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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