Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • fanOFhts
    started a topic Adaptive bandwidth KDE for NGS data

    Adaptive bandwidth KDE for NGS data

    Abstract

    Background

    High-throughput sequencing experiments can be viewed as measuring some sort of a "genomic signal" that may represent a biological event such as the binding of a transcription factor to the genome, locations of chromatin modifications, or even a background or control condition. Numerous algorithms have been developed to extract different kinds of information from such data. However, there has been very little focus on the reconstruction of the genomic signal itself. Such reconstructions may be useful for a variety of purposes ranging from simple visualization of the signals to sophisticated comparison of different datasets.

    Methods

    Here, we propose that adaptive-bandwidth kernel density estimators are well-suited for genomic signal reconstructions. This class of estimators is a natural extension of the fixed-bandwidth estimators that have been employed in several existing ChIP-Seq analysis programs.

    Results

    Using a set of ChIP-Seq datasets from the ENCODE project, we show that adaptive-bandwidth estimators have greater accuracy at signal reconstruction compared to fixed-bandwidth estimators, and that they have significant advantages in terms of visualization as well. For both fixed and adaptive-bandwidth schemes, we demonstrate that smoothing parameters can be set automatically using a held-out set of tuning data. We also carry out a computational complexity analysis of the different schemes and confirm through experimentation that the necessary computations can be readily carried out on a modern workstation without any significant issues.

    Background High-throughput sequencing experiments can be viewed as measuring some sort of a "genomic signal" that may represent a biological event such as the binding of a transcription factor to the genome, locations of chromatin modifications, or even a background or control condition. Numerous algorithms have been developed to extract different kinds of information from such data. However, there has been very little focus on the reconstruction of the genomic signal itself. Such reconstructions may be useful for a variety of purposes ranging from simple visualization of the signals to sophisticated comparison of different datasets. Methods Here, we propose that adaptive-bandwidth kernel density estimators are well-suited for genomic signal reconstructions. This class of estimators is a natural extension of the fixed-bandwidth estimators that have been employed in several existing ChIP-Seq analysis programs. Results Using a set of ChIP-Seq datasets from the ENCODE project, we show that adaptive-bandwidth estimators have greater accuracy at signal reconstruction compared to fixed-bandwidth estimators, and that they have significant advantages in terms of visualization as well. For both fixed and adaptive-bandwidth schemes, we demonstrate that smoothing parameters can be set automatically using a held-out set of tuning data. We also carry out a computational complexity analysis of the different schemes and confirm through experimentation that the necessary computations can be readily carried out on a modern workstation without any significant issues.

Latest Articles

Collapse

  • seqadmin
    Pathogen Surveillance with Advanced Genomic Tools
    by seqadmin




    The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
    03-24-2025, 11:48 AM
  • seqadmin
    New Genomics Tools and Methods Shared at AGBT 2025
    by seqadmin


    This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

    The Headliner
    The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
    03-03-2025, 01:39 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-20-2025, 05:03 AM
0 responses
49 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-19-2025, 07:27 AM
0 responses
57 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-18-2025, 12:50 PM
0 responses
50 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-03-2025, 01:15 PM
0 responses
201 views
0 reactions
Last Post seqadmin  
Working...