Search results for "Library complexity"

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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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