Journal
BIOINFORMATICS
Volume 32, Issue 1, Pages 43-49Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btv642
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Funding
- National Institutes of Health [T32-CA-140044]
- National Science Foundation [0903629]
- Prostate Cancer Foundation
- NATIONAL CANCER INSTITUTE [T32CA140044] Funding Source: NIH RePORTER
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Motivation: Discovery of novel splicing from RNA sequence data remains a critical and exciting focus of transcriptomics, but reduced alignment power impedes expression quantification of novel splice junctions. Results: Here, we profile performance characteristics of two-pass alignment, which separates splice junction discovery from quantification. Per sample, across a variety of transcriptome sequencing datasets, two-pass alignment improved quantification of at least 94% of simulated novel splice junctions, and provided as much as 1.7-fold deeper median read depth over those splice junctions. We further demonstrate that two-pass alignment works by increasing alignment of reads to splice junctions by short lengths, and that potential alignment errors are readily identifiable by simple classification. Taken together, two-pass alignment promises to advance quantification and discovery of novel splicing events.
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