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• W4311504141 abstract "Chromatin accessibility assays are central to the genome-wide identification of gene regulatory elements associated with transcriptional regulation. However, the data have highly variable quality arising from several biological and technical factors. To surmount this problem, we developed a sequence-based machine learning method to evaluate and refine chromatin accessibility data. Our framework, gapped k-mer SVM quality check (gkmQC), provides the quality metrics for a sample based on the prediction accuracy of the trained models. We tested 886 DNase-seq samples from the ENCODE/Roadmap projects to demonstrate that gkmQC can effectively identify high-quality (HQ) samples with low conventional quality scores owing to marginal read depths. Peaks identified in HQ samples are more accurately aligned at functional regulatory elements, show greater enrichment of regulatory elements harboring functional variants, and explain greater heritability of phenotypes from their relevant tissues. Moreover, gkmQC can optimize the peak-calling threshold to identify additional peaks, especially for rare cell types in single-cell chromatin accessibility data." @default.
• W4311504141 created "2022-12-26" @default.
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• W4311504141 date "2022-12-12" @default.
• W4311504141 modified "2023-10-01" @default.
• W4311504141 title "Quality assessment and refinement of chromatin accessibility data using a sequence-based predictive model" @default.
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• W4311504141 doi "https://doi.org/10.1073/pnas.2212810119" @default.
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• W4311504141 hasPublicationYear "2022" @default.
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