Sequencing data
ASAP: an environment for automated preprocessing of sequencing data
... of sequencing data so that researchers can quickly start their statistical analyses as well as incrementally add new data as is often necessary for large-scale research pro- ...sequence data, ...
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Adjusting for population stratification and relatedness with sequencing data
... GAW18 sequencing data containing 959 individuals and 8,348,674 single nucleotide variants (SNVs) across all 11 chromosomes, among which 2,791,923 SNVs were CVs and 3,977,003 were ...
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Overcoming bias and systematic errors in next generation sequencing data
... technologies, data from new high-throughput sequencing technologies are subject to technological and biological biases and systematic errors that can impact downstream ...
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On combining family and population based sequencing data
... family-based sequencing data to evaluate best practices using the Genetic Analysis Workshop 19 (GAW19) data ...genome sequencing and the other whole exome sequencing, we examined ...
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miRTrace reveals the organismal origins of microRNA sequencing data
... quencing data to their taxonomical origins, but similar methods exist for other data ...generation sequencing data, rather researchers extract DNA from samples of interest, PCR amplify the COI ...
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Gene based multiple trait analysis for exome sequencing data
... In next-generation sequencing data sets, huge num- bers of rare variants are genotyped across the whole genome. Because of the small number of observations for each rare variant, statistical tests for ...
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A goodness of fit association test for whole genome sequencing data
... different data and/or research results for ...genome sequencing and genome-wide association studies data of Genetic Analysis Workshop 18 for detecting true genetic ...
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Streamlined analysis of duplex sequencing data with Du Novo
... the data are filtered on MAF ...duplex sequencing data is that its under- lying infrastructure relies on high-performance resources provided by the Texas Advanced Computing Center (TACC) and the ...
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Exact association test for small size sequencing data
... In the Methods section, we provide a detailed descrip- tion of the EXAT statistic, and summarize how to compute p -values for significance testing. We then apply our EXAT to the analysis of targeted sequencing ...
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Genotype-Frequency Estimation from High-Throughput Sequencing Data
... Our evaluation of the performance of the proposed method with the low-coverage (mean 4 3 ) sequencing data on chro- mosome 6 for 81 individuals revealed 8,528,190 sites with minor-allele frequency (MAF) ...
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CHAPTER 5 Troubleshooting DNA Sequencing Data
... Dye primer and dye terminator sequencing data exhibit the same characteristics when samples fail to inject. Background is usually normal, and neither dye blobs of unincorporated terminator nor primer peak ...
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Characterization of background noise in capture based targeted sequencing data
... (WES) data sets from two independent studies that fragmented input DNA using acoustic shearing [47, ...WES data (Additional file 3: Figure S12b), but the degree of the increase was less prominent than that ...
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SeqBench: Integrated solution for the management and analysis of exome sequencing data
... next-generation sequencing (NGS) technologies has sparked a major revolution in biomedi- cal ...genomic sequencing data are now produced at an unprecedented ...in data management, computer ...
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GenomeGems: evaluation of genetic variability from deep sequencing data
... Deep Sequencing data generated in the Genome High-Throughput Sequencing Laboratory at Tel-Aviv University on the Illumina Gen- ome Analyzer ...of data produced from a number of samples, and ...
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Mitochondrial heteroplasmy in vertebrates using ChIP sequencing data
... ChIP-sequencing data for which mtDNA coverage has even been used as a control for background noise ...ChIP- sequencing data is a technical and not biological ...the data from Li et ...
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Differential correlation for sequencing data
... To identify miRNA–mRNA pairs that may change inter- actions due to tumor status, we evaluated miRNA and mRNA sequencing data from the TCGA database for breast cancer. Discordant was run with four different ...
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Visual programming for next-generation sequencing data analytics
... NGS data science (or analytics) is an interdisciplinary and critical field of bioinformat- ics research that has gained increased attention and visibility upon the explosion of NGS ...in sequencing yield ...
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Detection and classification of peaks in 5' cap RNA sequencing data
... omics data, identification of TSS regions remains a non-trivial ...of data were required [19] and this com- plexity translates into days of training on a computing cluster ...
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Analysis of error profiles in deep next generation sequencing data
... dilutions (1:1000 and 1:5000). For ploidy, 4v4 means 4 out of 4 allels are mutated in cancer cells, 2v4 means 2 out of 4 allele are mutated; 1v4 means 1 out of 4 alleles are mutated; 4v6 means 4 out of 6 alleles are ...
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SICTIN: Rapid footprinting of massively parallel sequencing data
... parallel sequencing is rapidly becoming the gold standard in hypothesis-free genome-wide studies of for instance transcription factor binding sites [1,2] histone modifications [3-5] and nucleosome positioning ...
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