Dataset Information
Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.
Ontology highlight
ABSTRACT: Unlabelled
: 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 naïve mapping.Availability and implementation
Ribomap is available as open source at http://www.cs.cmu.edu/?ckingsf/software/ribomapContact
carlk@cs.cmu.eduSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Wang H
PROVIDER: S-EPMC4908323 | biostudies-literature | 2016 Jun
REPOSITORIES: biostudies-literature
Publications
Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.
Bioinformatics (Oxford, England) 20160215 12
<h4>Unlabelled</h4>: 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 ori ...[more]