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

  • Date: Jul 18, 2018
  • Time: 02:00 PM - 03:00 PM (Local Time Germany)
  • Speaker: Celine Prakash from the Center for Integrative Bioinformatics Vienna, Austria
  • Location: MPI Plön
  • Room: Lecture hall
  • Host: Tobias Kaiser


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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