Long-Read Transcriptome Analysis at BioBam Bioinformatics
From November 3, 2024 to January 3, 2025, Yalan Bi, LongTREC Doctoral Candidate at the Max Planck Institute for Molecular Genetics, had the opportunity to carry out a research secondment at BioBam Bioinformatics, supervised by Stefan Götz. This secondment offered valuable growth, both in scientific expertise and personal development.
My goal? Learning to use BioBam’s OmicsBox for long-read transcriptome sequencing (LRTS) analysis, comparing transcriptome reconstruction methods across datasets, and learning how a bioinformatics company works and supports scientific research.
Yalan reflects on her experience:
What I Learned 🎓
I learned to analyse and visualise LRTS data in OmicsBox, and how BioBam organises its day-to-day activities, communicates between teams, and develops and maintains its software.
Takeaways 🌱
Using the LRGASP data, we compared transcriptomes reconstructed with IsoTools, developed by our group, and with IsoQuant and FLAIR, both integrated in OmicsBox. The same dataset reconstructed with different methods showed different levels of novelty. These novel transcripts could be true discoveries or technical artefacts. Balancing agreement with the reference annotation against discovery of novel transcripts is important, since the choice of reliable transcripts shapes gene models and all downstream analysis.
Impact 🌟
Based on how OmicsBox represents data, I implemented several transcript- and gene-level visualisation components in IsoTools, discussed with the BioBam team.
Overall, this secondment combined method comparison, software development and insight into how a bioinformatics company operates.
