ArticleBioinformatics (Oxford, England)2019
CoCo: RNA-seq read assignment correction for nested genes and multimapped reads.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
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- Trichomes and unique gene expression confer insect herbivory resistance in Vitis labrusca grapevines.BMC plant biology · 2024Article
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- Multi-omics in nasal epithelium reveals three axes of dysregulation for asthma risk in the African Diaspora populations.Nature communications · 2024Article
- Gene-expression profiling of individuals resilient to Alzheimer's disease reveals higher expression of genes related to metallothionein and mitochondrial processes and no changes in the unfolded protein response.Acta neuropathologica communications · 2024Article
- Comprehensive map of ribosomal 2'-O-methylation and C/D box snoRNAs in Drosophila melanogaster.Nucleic acids research · 2024Article
- Isocitrate dehydrogenase wt and IDHmut adult-type diffuse gliomas display distinct alterations in ribosome biogenesis and 2'O-methylation of ribosomal RNA.Neuro-oncology · 2023Article
- Osteoclast microRNA Profiling in Rheumatoid Arthritis to Capture the Erosive Factor.JBMR plus · 2023Article
- Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences.Genome biology · 2023Article
- Small RNAs and Karma methylation in Elaeis guineensis mother palms are linked to high clonal mantling.Plant molecular biology · 2023Article
- Altered tRNA processing is linked to a distinct and unusual La protein in Tetrahymena thermophila.Nature communications · 2022Article
- Chromosome-level genome assembly of Mentha longifolia L. reveals gene organization underlying disease resistance and essential oil traits.G3 (Bethesda, Md.) · 2022Article
- The snoGloBe interaction predictor reveals a broad spectrum of C/D snoRNA RNA targets.Nucleic acids research · 2022Article
- High-grade ovarian cancer associated H/ACA snoRNAs promote cancer cell proliferation and survival.NAR cancer · 2022Article
- MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts.BMC bioinformatics · 2022Article
- Phylogenetic and Molecular Analyses Identify SNORD116 Targets Involved in the Prader-Willi Syndrome.Molecular biology and evolution · 2022Article
- miR profile in pagetic osteoclasts: from large-scale sequencing to gene expression study.Journal of molecular medicine (Berlin, Germany) · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationNext-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.
resultsHere 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. AVAILABILITY AND IMPLEMENTATION: The CoCo software is an open source package written in Python and available from http://gitlabscottgroup.med.usherbrooke.ca/scott-group/coco. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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