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Correcting nucleotide-specific biases in high-throughput sequencing data

Jeremy R. Wang, Bryan Quach, Terrence S. Furey
2017 BMC Bioinformatics  
High-throughput sequence (HTS) data exhibit position-specific nucleotide biases that obscure the intended signal and reduce the effectiveness of these data for downstream analyses.  ...  Results: We present a novel method to detect and correct position-specific nucleotide biases in HTS short read data.  ...  Availability of data and materials DNase-seq, ChIP-seq, FAIRE-seq, and ATAC-seq data from GM12878, K562, and H1-hESC cell lines were used from the Encyclopedia of DNA Elements (ENCODE) project (https:/  ... 
doi:10.1186/s12859-017-1766-x pmid:28764645 pmcid:PMC5540620 fatcat:mgz6nzun5nhjnf7au27migcede

Analysis of sequencing data for probing RNA secondary structures and protein–RNA binding in studying posttranscriptional regulations

Xihao Hu, Yang Wu, Zhi John Lu, Kevin Y. Yip
2015 Briefings in Bioinformatics  
Key Words  RNA secondary structure  Protein-RNA interactions  RNA binding motifs  High-throughput sequencingData analysis  ...  In the study of RNA secondary structures using high-throughput sequencing, bases are modified or cleaved according to their structural features, which alter the resulting composition of sequencing reads  ...  Biases in the high-throughput experimental data Like other techniques, data from RIP-and CLIP-based experiments contain biases that are usually corrected in multiple steps [44, 48, 49] .  ... 
doi:10.1093/bib/bbv106 pmid:26655457 fatcat:enq72a3cqras7mpjyvu7ai25jq

Overcoming bias and systematic errors in next generation sequencing data

Margaret A Taub, Hector Corrada Bravo, Rafael A Irizarry
2010 Genome Medicine  
As is the case for microarrays and other high-throughput technologies, data from new high-throughput sequencing technologies are subject to technological and biological biases and systematic errors that  ...  High-throughput sequencing involves the parallel sequen cing of millions of DNA fragments simultaneously.  ...  Coverage biases Another long-observed phenomenon of high-throughput sequencing data is the strong, reproducible effect of local sequence content on the coverage of a genomic region by sequencing reads  ... 
doi:10.1186/gm208 pmid:21144010 pmcid:PMC3025429 fatcat:unvc2hplnnes7ej2hv3aao55bq

Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis [article]

Umit Akkose, Ogun Adebali
2022 bioRxiv   pre-print
Boquila uses standard file formats for input and output data, and it can be easily integrated into any workflow for high-throughput sequencing applications.  ...  Therefore, Genome-wide NGS reads biased towards specific nucleotide profiles are affected by the genome-wide heterogeneous nucleotide distribution.  ...  FASTA and FASTQ are standard formats for high-throughput sequencing reads, making boquila easier to integrate into existing workflows.  ... 
doi:10.1101/2022.03.29.486262 fatcat:dqwhcwapvfaj3jnbjt3hjwcxwe

Workshop: Inference of allele specific expression levels from RNA-Seq data

Sahar Al Seesi, Ion Mandoiu
2012 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS)  
Most current methods for estimating gene/isoform expression levels from high-throughput whole transcriptome sequencing (RNA-Seq) data rely on mapping the reads to a reference genome and/or transcriptome  ...  biases introduced by library preparation and sequencing protocols.  ...  Most current methods for estimating gene/isoform expression levels from high-throughput whole transcriptome sequencing (RNA-Seq) data rely on mapping the reads to a reference genome and/or transcriptome  ... 
doi:10.1109/iccabs.2012.6182666 dblp:conf/iccabs/SeesiM12 fatcat:fx7z46eayzhkfnukqfsdzxtju4

Canonical A-to-I and C-to-U RNA Editing Is Enriched at 3′UTRs and microRNA Target Sites in Multiple Mouse Tissues

Tongjun Gu, Frank W. Buaas, Allen K. Simons, Cheryl L. Ackert-Bicknell, Robert E. Braun, Matthew A. Hibbs, Nina Papavasiliou
2012 PLoS ONE  
possible base substitutions) is an artifact of current high-throughput sequencing technology.  ...  Further, we report that high-confidence canonical RNA editing sites can cause non-synonymous amino acid changes and are significantly enriched in 39 UTRs, specifically at microRNA target sites, suggesting  ...  Given the large number of observed non-canonical editing sites that show a strand bias in our RNA-seq data and given that systematic high-throughput sequencing biases appear to be quite common [15] ,  ... 
doi:10.1371/journal.pone.0033720 pmid:22448268 pmcid:PMC3308996 fatcat:54v6mqhxifbnrk6md2ciaouz7a

Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions

André L Martins, Ninad M Walavalkar, Warren D Anderson, Chongzhi Zang, Michael J Guertin
2017 Nucleic Acids Research  
Coupling molecular biology to high-throughput sequencing has revolutionized the study of biology.  ...  We developed seqOutBias to characterize enzymatic sequence bias from experimental data and scale individual sequence reads to correct intrinsic enzymatic sequence biases.  ...  PRO-seq couples terminating nuclear run-on assays with high-throughput sequencing to quantify engaged RNA polymerase molecules genome-wide at nucleotide resolution (4) .  ... 
doi:10.1093/nar/gkx1053 pmid:29126307 pmcid:PMC5778497 fatcat:ci2nlk4scrbphc43hzxrp2vfae

HTS-IBIS: fast and accurate inference of binding site motifs from HT-SELEX data [article]

Yaron Orenstein, Ron Shamir
2015 bioRxiv   pre-print
HTS-IBIS corrects for technological biases, selects the cycle and k, and builds a motif starting from a consensus k-mer in that cycle.  ...  High-throughput-SELEX measures protein-DNA binding by deep sequencing over several cycles of enrichment. We devised a new algorithm called HTS-IBIS for the inference task.  ...  Additionally, in (Orenstein and Shamir 2014) we identified systematic biases in k-mer frequencies in HTS data. We address such biases here using the observation that they are strand-specific.  ... 
doi:10.1101/022277 fatcat:3xeo5qz4svhchmwnowadwjnyii

Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments

Ekaterina E Khrameeva, Mikhail S Gelfand
2012 BMC Bioinformatics  
High-throughput sequencing of whole genomes and transcriptomes allows one to generate large amounts of sequence data very rapidly and at a low cost.  ...  Gene coverage profiles showed laboratory-specific non-uniformity that survived the 3'-bias correction and mappability normalization, suggesting that there are other yet unknown mRNA-associated biases.  ...  High-throughput sequencing of whole genomes and transcriptomes has become a major focus of modern biology as DNA sequencing is now available to many more projects, and even single research groups.  ... 
doi:10.1186/1471-2105-13-s6-s4 pmid:22537043 pmcid:PMC3358657 fatcat:d6f2cnoaxzasvfayn5yekuxv3a

Frequency Analysis Techniques for Identification of Viral Genetic Data

V. Trifonov, R. Rabadan
2010 mBio  
The low costs and high throughput of sequencing technologies are expected to allow for the genetic material in those samples to be sequenced and the genomes of the novel microorganisms to be identified  ...  The low costs and high throughput of sequencing technologies provide a method for the identification of novel microorganisms by sequence alignment.  ...  In some cases, frequency analysis could be the only viable way of detecting genetic relationships in data obtained from high-throughput sequencing experiments.  ... 
doi:10.1128/mbio.00156-10 pmid:20824103 pmcid:PMC2932508 fatcat:w7nmthsk5bgh5oyeljm5elalvu

Systematic bias in high-throughput sequencing data and its correction by BEADS

Ming-Sin Cheung, Thomas A. Down, Isabel Latorre, Julie Ahringer
2011 Nucleic Acids Research  
To correct sequence bias, we present BEADS (bias elimination algorithm for deep sequencing), a simple three-step normalization scheme that successfully unmasks real binding patterns in ChIP-seq data.  ...  We have focused on data obtained from Illumina's Genome Analyser platform, where at least three factors contribute to sequence bias: GC content, mappability of sequencing reads, and regional biases that  ...  ACKNOWLEDGEMENTS The authors thank Raymond Auerbach for the human input sequence data and Oliver Hobert for the C. elegans genomic DNA sequence data.  ... 
doi:10.1093/nar/gkr425 pmid:21646344 pmcid:PMC3159482 fatcat:gjfatiwibngmpevrltjotiax3i

Bias detection and correction in RNA-Sequencing data

Wei Zheng, Lisa M Chung, Hongyu Zhao
2011 BMC Bioinformatics  
High throughput sequencing technology provides us unprecedented opportunities to study transcriptome dynamics.  ...  levels from RNA-Seq data, such as reads per kilobase of gene length per million reads (RPKM), are biased in terms of gene length, GC content and dinucleotide frequencies.  ...  Research was funded by in part by the National Institutes of Health (NIH) grants to the authors.  ... 
doi:10.1186/1471-2105-12-290 pmid:21771300 pmcid:PMC3149584 fatcat:6khpgy5f3fafjcpkyw6yv55x34

Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions [article]

Andre L. Martins, Ninad M. Walavalkar, Warren D. Anderson, Chongzhi Zang, Michael J. Guertin
2017 bioRxiv   pre-print
Coupling molecular biology to high throughput sequencing has revolutionized the study of biology.  ...  We developed seqOutBias to characterize enzymatic sequence bias from experimental data and scale individual sequence reads to correct intrinsic enzymatic sequence biases.  ...  PRO-seq couples terminating nuclear run-on assays with high throughput sequencing to quantify engaged RNA polymerase molecules genome-wide at nucleotide resolution (4) .  ... 
doi:10.1101/104364 fatcat:re4hxsotgvasta37mbyiuvho3y

Cross-hybridization modeling on Affymetrix exon arrays

Karen Kapur, Hui Jiang, Yi Xing, Wing Hung Wong
2008 Computer applications in the biosciences : CABIOS  
Comparison with Solexa ultra high-throughput sequencing data demonstrates that correction for cross-hybridization leads to a significant improvement of gene expression estimates.  ...  These arrays have the potential to achieve quantitative high-throughput estimates of transcript abundances, but currently these estimates are affected by biases due to cross-hybridization, in which probes  ...  ACKNOWLEDGMENTS We thank Barbara Wold's lab for making the Solexa sequencing data available and Zhengqing Ouyang, Xi Chen and Xiao Tong for discussions.  ... 
doi:10.1093/bioinformatics/btn571 pmid:18984598 pmcid:PMC2639301 fatcat:cghjj4ksjfcpddzcbj4cuwhk3u

Genotype Calling from Population-Genomic Sequencing Data

Takahiro Maruki, Michael Lynch
2017 G3: Genes, Genomes, Genetics  
To take full advantage of the resultant information, we have developed maximum-likelihood (ML) methods for calling genotypes from high-throughput sequencing data.  ...  We applied the proposed method to high-coverage (mean 18·) sequencing data of 83 clones from a population of Daphnia pulex.  ...  Here, the genotype of an individual at a single site is called from the nucleotide read quartet (counts of A, C, G, and T) of high-throughput sequencing data at the site by an ML method.  ... 
doi:10.1534/g3.117.039008 pmid:28108551 pmcid:PMC5427492 fatcat:vya54ob7dze43a7rxiopievuj4
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