0000000000424729

AUTHOR

Matthias Truss

showing 2 related works from this author

Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus

2016

Background: ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal using random barcodes. However, the use of random barcodes requires additional preprocessing of the mapping data, which complicates the computational analysis. To date, only a very limited number of software packages are available for the analysis of ChIP-exo data, which have not yet been systematically tested and compared on ChIP-nexus data. Results: Here, we present a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal …

0301 basic medicineFOS: Computer and information sciencesDuplication ratesChromatin ImmunoprecipitationBioinformaticsPipeline (computing)610Biologycomputer.software_genre600 Technik Medizin angewandte Wissenschaften::610 Medizin und Gesundheit03 medical and health sciencesSoftwareChIP-nexusGeneticsPreprocessorNucleotide MotifsLibrary complexityChIP-exoGeneticsProtocol (science)Binding Sitesbusiness.industryfungiComputational BiologyHigh-Throughput Nucleotide SequencingReproducibility of ResultsChipChromatin immunoprecipitationData mappingDNA-Binding ProteinsAlgorithm030104 developmental biologyChIP-exoData miningbusinessPeak callingcomputerAlgorithmsSoftwareProtein BindingTranscription FactorsResearch ArticleBiotechnologyBMC Genomics
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Additional file 1 of Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus

2016

Supplementary figures and tables. The following additional data are available with the online version of this paper. Additional data file 1 contains an explanatory figure for duplication levels as well as figures and tables for additional analyses including duplication rate plots, examples for mapping artifacts, 5â end coverage around motif centered binding sites, cross-correlation plots, qfrag-length distributions, scatterplots of signal scores of overlapping peaks and corresponding IDR plots, as well as two tables containing the total numbers of overlapping peaks and overlapping peaks with IDR â ¤ 0.01 for all pairs of biological replicates. (PDF 3840 kb)

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