@article {Wang017509, author = {Hao Wang and Joel McManus and Carl Kingsford}, title = {Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abundance with Ribomap}, elocation-id = {017509}, year = {2015}, doi = {10.1101/017509}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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.}, URL = {https://www.biorxiv.org/content/early/2015/04/04/017509}, eprint = {https://www.biorxiv.org/content/early/2015/04/04/017509.full.pdf}, journal = {bioRxiv} }