ArticleBMC bioinformatics2017
mmquant: how to count multi-mapping reads?
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- A fusarioid fungus forms mutualistic interactions with poplar trees that resemble ectomycorrhizal symbiosis.IMA fungus · 2025Article
- Accurate allocation of multimapped reads enables regulatory element analysis at repeats.Genome research · 2024Article
- Intraspecific diploidization of a halophyte root fungus drives heterosis.Nature communications · 2024Article
- Evolution of sex-biased genes inEcology and evolution · 2024Article
- Methylated guanosine and uridine modifications inRSC chemical biology · 2023Article
- High-quality read-based phasing of cystic fibrosis cohort informs genetic understanding of disease modification.HGG advances · 2023Article
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- The transcriptomics profiling of blood CD4 and CD8 T-cells in narcolepsy type I.Frontiers in immunology · 2023Article
- srnaMapper: an optimal mapping tool for sRNA-Seq reads.BMC bioinformatics · 2022Article
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- Rta is the principal activator of Epstein-Barr virus epithelial lytic transcription.PLoS pathogens · 2022Article
- Alpinetin promotes hair regeneration via activating hair follicle stem cells.Chinese medicine · 2022Article
- Accurate Quantification of Overlapping Herpesvirus Transcripts from RNA Sequencing Data.Journal of virology · 2022Article
- MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts.BMC bioinformatics · 2022Article
- Transcriptomic profiling ofInnate immunity · 2021Article
- Identification and Validation of Reference Genes inFrontiers in microbiology · 2021Article
- Article
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1 author.
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Abstract
backgroundRNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used (drop duplicated genes, distribute uniformly the reads, or estimate expression), but all of them provide biased results.
resultsWe provide here a tool, called mmquant, for computing gene expression, included duplicated genes. If a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes.
conclusionmmquant is a drop-in replacement of the widely used tools htseq-count and featureCounts that handles multi-mapping reads in an unabiased way.
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