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
Abstract:
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.