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Making the Most of Your NGS Data: Understanding Metrics
https://sequencing.roche.com/us/en/article-listing/metrics-for-target-enriched-ngs.html
WEBThe duplication rate is the fraction of mapped reads marked as duplicate reads in a particular data set. In contrast to overlapping reads, duplicate reads offer no additional information and are removed from sequencing data during bioinformatic analysis, a process known as deduplication.
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Ask a Scientist: What is Duplication Rate in NGS? - YouTube
https://www.youtube.com/watch?v=6ZJfZAdR_q0
WEBAug 21, 2020 · 4.7K views 3 years ago Ask a Scientist. How does duplication rate affect the quality of NGS data, and what can be done to minimize duplicate reads? This video describes what duplicate reads...
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Multiplexed targeted next generation sequencing coverage | IDT
https://www.idtdna.com/pages/education/decoded/article/minimizing-duplicates-and-obtaining-uniform-coverage-in-multiplexed-target-enrichment-sequencing
WEBMar 20, 2018 · The duplication rate is the fraction of mapped reads where any 2 reads share the same 5′ and 3′ coordinates. Duplicates mostly arise from the PCR step during library construction. Duplicates may also result in artifacts on the sequencing instrument where the same template binds to multiple clusters on a flow cell.
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How PCR duplicates arise in next-generation sequencing
https://www.cureffi.org/2012/12/11/how-pcr-duplicates-arise-in-next-generation-sequencing/
WEBDec 11, 2012 · Higher rates of PCR duplicates e.g. 30% arise when people have too little starting material such that greater amplification of the library is needed in step 3, or when people have too great a variance in fragment size, such that smaller fragments, which are easier to PCR amplify, end up over-represented.
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RNA-seq: Basic Bioinformatics Analysis - PMC - National Center …
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168365/
WEBRNA-seq alignments can have a higher duplication rate than many other NGS applications, including whole-genome sequencing, ChIP-seq, ATAC-seq, etc. Typical duplication rates range from 30% to 90%, often depending on sequencing depth and transcriptome size.
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Mechanisms of Gene Duplication and Amplification - PMC
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4315931/
WEBDuplication by exchanges between sister chromosomes. ( A) a and b are sequence elements between which exchanges can be mediated by recombination, annealing, or transposition. Hybrid elements (b/a or a/b) are left at the rearrangement junctions. Duplications are subject to remodeling deletions that remove the junction.
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On the causes, consequences, and avoidance of PCR duplicates: …
https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13800
WEBApr 16, 2023 · TABLE 1. PCR duplicate rates across sequencing technologies. PCR duplicates create a distorted view of the abundancies of molecules in the original sample, which may bias or degrade downstream statistical analyses (Casbon et al., 2011; DePristo et al., 2011; Fu et al., 2018; Niu et al., 2019 ).
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PCR Duplicate Proportion Estimation and Consequences for DNA …
https://link.springer.com/chapter/10.1007/978-3-031-12766-3_18
WEBNov 29, 2022 · Therefore, our calculations that follow will take the direct observation at the SNP loci as the combined PCR and fragmentation duplicate rate. In total, 78, 173 sets of duplicates are observed across our 22 samples, with …
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A computational method for estimating the PCR duplication rate …
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1471-9
WEBMar 14, 2017 · The PCR duplication rate of these datasets was 1–9% lower than the read duplication rate across the 40 exome datasets (Additional file 1: Table S1). This indicated that only a small fraction of the read duplicates correspond to natural read duplicates.
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Elimination of PCR duplicates in RNA-seq and small RNA-seq …
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4933-1
WEBPublished: 13 July 2018. Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers. Yu Fu, Pei-Hsuan Wu, Timothy Beane, Phillip D. Zamore & Zhiping Weng. BMC Genomics 19, Article number: 531 ( 2018 ) Cite this article. 28k Accesses. 88 Citations. 12 Altmetric. Metrics. Abstract. Background.
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