RT Journal Article
SR Electronic
T1 Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abundance with Ribomap
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 017509
DO 10.1101/017509
A1 Hao Wang
A1 Joel McManus
A1 Carl Kingsford
YR 2015
UL http://biorxiv.org/content/early/2015/04/04/017509.abstract
AB Ribosome profiling is a recently developed high-throughput sequencing technique that captures approximately 30 bp long ribosome-protected mRNA fragments during translation. Because of alternative splicing and repetitive sequences, a ribosome-protected read may map to many places in the transcriptome, leading to discarded or arbitrary mappings when standard approaches are used. We present a technique and software that addresses this problem by assigning reads to potential origins proportional to estimated transcript abundance. This yields a more accurate estimate of ribosome profiles compared with a naϊve mapping. Ribomap is available as open source at http://www.cs.cmu.edu/∼ckingsf/software/ribomap.