ArticleBioinformatics (Oxford, England)2011
The uniqueome: a mappability resource for short-tag sequencing.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework.Genome biology · 2024Article
- CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data.PLoS computational biology · 2022Article
- GenMap: ultra-fast computation of genome mappability.Bioinformatics (Oxford, England) · 2020Article
- Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae.Scientific reports · 2019Article
- Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize.Genome biology · 2017Article
- Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes.Scientific reports · 2017Article
- Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.Briefings in bioinformatics · 2017Review
- Whole exome association of rare deletions in multiplex oral cleft families.Genetic epidemiology · 2017Article
- TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells.Genome biology · 2016Article
- Joint detection of copy number variations in parent-offspring trios.Bioinformatics (Oxford, England) · 2016Article
- Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments.Nucleic acids research · 2015Article
- EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.Bioinformatics (Oxford, England) · 2015Article
- Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.BMC genomics · 2015Article
- Precise correction of the dystrophin gene in duchenne muscular dystrophy patient induced pluripotent stem cells by TALEN and CRISPR-Cas9.Stem cell reports · 2015Article
- Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data.PloS one · 2015Article
- Article
- Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads.BMC genomics · 2014Article
- Sequence profiling of the Saccharomyces cerevisiae genome permits deconvolution of unique and multialigned reads for variant detection.G3 (Bethesda, Md.) · 2014Article
- Imperfect centered miRNA binding sites are common and can mediate repression of target mRNAs.Genome biology · 2014Article
- Minor class splicing shapes the zebrafish transcriptome during development.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryQuantification applications of short-tag sequencing data (such as CNVseq and RNAseq) depend on knowing the uniqueness of specific genomic regions at a given threshold of error. Here, we present the 'uniqueome', a genomic resource for understanding the uniquely mappable proportion of genomic sequences. Pre-computed data are available for human, mouse, fly and worm genomes in both color-space and nucletotide-space, and we demonstrate the utility of this resource as applied to the quantification of RNAseq data. AVAILABILITY: Files, scripts and supplementary data are available from http://grimmond.imb.uq.edu.au/uniqueome/; the ISAS uniqueome aligner is freely available from http://www.imagenix.com/.
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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.