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Alexander Petri: Algorithms for long read transcriptome analysis

Time: Wed 2023-03-22 13.30 - 14.30

Location: Albano, Cramer room

Participating: Alexander Petri

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Advances in long-read transcriptome sequencing enable us to fully sequence transcripts, which greatly improves our ability to study transcription processes. One popular long-read transcriptome sequencing technique is Oxford Nanopore Technologies (ONT), which through its cost-effective sequencing and high throughput, has the potential to characterize the full transcriptome in a cell. On the other hand, due to transcript variability and sequencing errors, long cDNA reads need substantial bioinformatic processing to produce a set of isoform predictions from the original reads. Especially the separation of mutations and sequencing errors for higher error rates in reads poses a complex problem. During my PHD I attempt to tackle the problems described above especially for the analysis of transcriptomic data. I will describe our approach to predicting transcripts from a set of ONT sequencing reads without relying on a reference.