ArticleBioinformatics (Oxford, England)2016
MMR: a tool for read multi-mapper resolution.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
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- Predicting RNA splicing from DNA sequence using Pangolin.Genome biology · 2022Article
- O-linked α2,3 sialylation defines stem cell populations in breast cancer.Science advances · 2022Article
- An effective method to resolve ambiguous bisulfite-treated reads.BMC bioinformatics · 2021Article
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- The Sophisticated Transcriptional Response Governed by Transposable Elements in Human Health and Disease.International journal of molecular sciences · 2020Review
- Mobile genomics: tools and techniques for tackling transposons.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Review
- Handling multi-mapped reads in RNA-seq.Computational and structural biotechnology journal · 2020Review
- Multimapping confounds ribosome profiling analysis: A case-study of the Hsp90 molecular chaperone.Proteins · 2020Article
- mmannot: How to improve small-RNA annotation?PloS one · 2020Article
- Acute systemic inflammatory response to lipopolysaccharide stimulation in pigs divergently selected for residual feed intake.BMC genomics · 2019Article
- Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression.PLoS computational biology · 2019Article
- Is it time to change the reference genome?Genome biology · 2019Article
- Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis.Genome biology · 2019Article
- The Primary Antisense Transcriptome ofGenes · 2019Article
- Gene Expression Pattern and Regulatory Network ofInternational journal of genomics · 2019Article
- Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines.Mobile DNA · 2019Article
- Production of Protein-Complex Components Is Stoichiometric and Lacks General Feedback Regulation in Eukaryotes.Cell systems · 2018Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationMapping high-throughput sequencing data to a reference genome is an essential step for most analysis pipelines aiming at the computational analysis of genome and transcriptome sequencing data. Breaking ties between equally well mapping locations poses a severe problem not only during the alignment phase but also has significant impact on the results of downstream analyses. We present the multi-mapper resolution (MMR) tool that infers optimal mapping locations from the coverage density of other mapped reads.
resultsFiltering alignments with MMR can significantly improve the performance of downstream analyses like transcript quantitation and differential testing. We illustrate that the accuracy (Spearman correlation) of transcript quantification increases by 15% when using reads of length 51. In addition, MMR decreases the alignment file sizes by more than 50%, and this leads to a reduced running time of the quantification tool. Our efficient implementation of the MMR algorithm is easily applicable as a post-processing step to existing alignment files in BAM format. Its complexity scales linearly with the number of alignments and requires no further inputs. AVAILABILITY AND IMPLEMENTATION: Open source code and documentation are available for download at http://github.com/ratschlab/mmr Comprehensive testing results and further information can be found at http://bioweb.me/mmr. CONTACT: andre.kahles@ratschlab.org or gunnar.ratsch@ratschlab.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.