NGS-Integrator: An efficient tool for combining multiple NGS data tracks using minimum Bayes' factors.

BMC Genomics
Bronte WenMark A Knepper

Abstract

Next-generation sequencing (NGS) is widely used for genome-wide identification and quantification of DNA elements involved in the regulation of gene transcription. Studies that generate multiple high-throughput NGS datasets require data integration methods for two general tasks: 1) generation of genome-wide data tracks representing an aggregate of multiple replicates of the same experiment; and 2) combination of tracks from different experimental types that provide complementary information regarding the location of genomic features such as enhancers. NGS-Integrator is a Java-based command line application, facilitating efficient integration of multiple genome-wide NGS datasets. NGS-Integrator first transforms all input data tracks using the complement of the minimum Bayes' factor so that all values are expressed in the range [0,1] representing the probability of a true signal given the background noise. Then, NGS-Integrator calculates the joint probability for every genomic position to create an integrated track. We provide examples using real NGS data generated in our laboratory and from the mouse ENCODE database. Our results show that NGS-Integrator is both time- and memory-efficient. Our examples show that NGS-Integrator ca...Continue Reading

References

Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Nov 4, 2008·Nature Biotechnology·Hongkai JiWing H Wong
Jan 6, 2009·Nature Biotechnology·Joel RozowskyMark B Gerstein
Feb 5, 2009·Proceedings of the National Academy of Sciences of the United States of America·Ming-Jiun YuMark A Knepper
Apr 27, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jialin Xu, Yu Zhang
May 5, 2012·Nucleus·Salvatore Spicuglia, Laurent Vanhille
Sep 1, 2012·Nature Protocols·Jianxing FengXiaole Shirley Liu
Oct 12, 2016·Scientific Reports·Pablo C SandovalMark A Knepper
Oct 5, 2017·Proceedings of the National Academy of Sciences of the United States of America·Kiyoshi IsobeMark A Knepper
Mar 25, 2018·Journal of the American Society of Nephrology : JASN·Hyun Jun JungMark A Knepper

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Citations

Jul 27, 2021·American Journal of Physiology. Renal Physiology·Hiroaki KikuchiMark A Knepper

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Methods Mentioned

BETA
RNA-Seq
ChIP-Seq
ATAC-Seq
immunoprecipitation
acetylation

Software Mentioned

NGS
UCSC genome browser
Linux
BigWig
Integrator
Calculator
- Integrator Calculator
bedGraph
Integrator ‘ Calculator
samtools

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