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bioRxiv · 10.1101/017509

Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abundance with Ribomap

Hao Wang·Joel McManus·Carl Kingsford
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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 na{iota}ve mapping. Ribomap is available as open source at http://www.cs.cmu.edu/[~]ckingsf/software/ribomap.

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Hao Wang, Joel McManus, Carl Kingsford. 2015-04-04. Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abundance with Ribomap. https://doi.org/10.1101/017509

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