Special Seminar - Celine Prakash: A simple model for fragmentation patterns in RNA sequencing provides insights into the expected coverage profile

  • Datum: 18.07.2018
  • Uhrzeit: 14:00 - 15:00
  • Vortragende(r): Celine Prakash vom Center for Integrative Bioinformatics in Wien, Österreich
  • Mehr Informationen über die Vortragende finden Sie hier: http://www.cibiv.at/~celine/
  • Ort: MPI Plön
  • Raum: Hörsaal
  • Gastgeber: Tobias Kaiser

Abstract (auf Englisch):

In most RNA-seq technologies, sequencing the full length of RNA molecules requires fragmentation into smaller pieces. To investigate the expected coverage after fragmentation, we develop a simple enumerative combinatorics fragmentation model that is independent of bias from the experimental method and is not specific to the transcript sequence. We utilize the model to understand how factors such as fragment length to transcript length ratio, read length to fragment length ratio, fragment length distribution, method of fragmentation and number of molecules influence the variability of coverage across a transcript.

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