Journal
BIOINFORMATICS
Volume 35, Issue 23, Pages 5039-5047Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btz433
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Funding
- Natural Sciences and Engineering Research Council of Canada (NSERC) [RGPIN-2018-05412]
- Canada Research Chair in RNA Biology and Cancer Genomics
- Fonds de Recherche du Quebec Sante (FRQS) Research Scholar Junior 2 Career Award
- NSERC
- FRQS
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Motivation: Next-generation sequencing techniques revolutionized the study of RNA expression by permitting whole transcriptome analysis. However, sequencing reads generated from nested and multi-copy genes are often either misassigned or discarded, which greatly reduces both quantification accuracy and gene coverage. Results: Here we present count corrector (CoCo), a read assignment pipeline that takes into account the multitude of overlapping and repetitive genes in the transcriptome of higher eukaryotes. CoCo uses a modified annotation file that highlights nested genes and proportionally distributes multimapped reads between repeated sequences. CoCo salvages over 15% of discarded aligned RNA-seq reads and significantly changes the abundance estimates for both coding and non-coding RNA as validated by PCR and bedgraph comparisons.
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