DOI: 10.1101/477869Nov 29, 2018Paper

CoCo: RNA-seq Read Assignment Correction for Nested Genes and Multimapped Reads

BioRxiv : the Preprint Server for Biology
Gabrielle Deschamps-FrancoeurMichelle S Scott


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 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. Availability: The CoCo software is an open source package written in Python and available from

Related Concepts

Polymerase Chain Reaction
Computer Software
RNA, Untranslated
Sequence Determinations, RNA
Nested Genes
Protein Expression

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