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عنوان
A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments.

پدید آورنده
Bansal, Vikas

موضوع

رده

کتابخانه
Center and Library of Islamic Studies in European Languages

محل استقرار
استان: Qom ـ شهر: Qom

Center and Library of Islamic Studies in European Languages

تماس با کتابخانه : 32910706-025

NATIONAL BIBLIOGRAPHY NUMBER

Number
LA1690178z

TITLE AND STATEMENT OF RESPONSIBILITY

Title Proper
A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments.
General Material Designation
[Article]
First Statement of Responsibility
Bansal, Vikas

SUMMARY OR ABSTRACT

Text of Note
PCR amplification is an important step in the preparation of DNA sequencing libraries prior to high-throughput sequencing. PCR amplification introduces redundant reads in the sequence data and estimating the PCR duplication rate is important to assess the frequency of such reads. Existing computational methods do not distinguish PCR duplicates from "natural" read duplicates that represent independent DNA fragments and therefore, over-estimate the PCR duplication rate for DNA-seq and RNA-seq experiments.In this paper, we present a computational method to estimate the average PCR duplication rate of high-throughput sequence datasets that accounts for natural read duplicates by leveraging heterozygous variants in an individual genome. Analysis of simulated data and exome sequence data from the 1000 Genomes project demonstrated that our method can accurately estimate the PCR duplication rate on paired-end as well as single-end read datasets which contain a high proportion of natural read duplicates. Further, analysis of exome datasets prepared using the Nextera library preparation method indicated that 45-50% of read duplicates correspond to natural read duplicates likely due to fragmentation bias. Finally, analysis of RNA-seq datasets from individuals in the 1000 Genomes project demonstrated that 70-95% of read duplicates observed in such datasets correspond to natural duplicates sampled from genes with high expression and identified outlier samples with a 2-fold greater PCR duplication rate than other samples.The method described here is a useful tool for estimating the PCR duplication rate of high-throughput sequence datasets and for assessing the fraction of read duplicates that correspond to natural read duplicates. An implementation of the method is available at https://github.com/vibansal/PCRduplicates .

SET

Date of Publication
2017
Title
UC San Diego

ELECTRONIC LOCATION AND ACCESS

Electronic name
 مطالعه متن کتاب 

[Article]
278119

a
Y

Proposal/Bug Report

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