Abstract
BackgroundATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the tools provide a comprehensive set of functionalities for preprocessing and quality assessment of aligned ATAC-seq datasets.ResultsWe have developed a Bioconductor package, ATACseqQC, for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling. Here we demonstrate the utilities of our package using 25 publicly available ATAC-seq datasets from four studies. We also provide guidelines on what the diagnostic plots should look like for an ideal ATAC-seq dataset.ConclusionsThis software package has been used successfully for preprocessing and assessing several in-house and public ATAC-seq datasets. Diagnostic plots generated by this package will facilitate the quality assessment of ATAC-seq data, and help researchers to evaluate their own ATAC-seq experiments as well as select high-quality ATAC-seq datasets from public repositories such as GEO to avoid generating hypotheses or drawing conclusions from low-quality ATAC-seq experiments. The software, source code, and documentation are freely available as a Bioconductor package at https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html.
Highlights
ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility
To help researchers quickly assess the quality of their ATAC-seq datasets, we have implemented a comprehensive set of functionalities in ATACseqQC
Before performing downstream quality assessment and other analysis, the resulting read alignments are evaluated and filtered using the bamQC function in the ATACseqQC package or external tools, such as SAMtools [36], to remove identical alignments most likely resulting from Polymerase Chain Reaction (PCR)/optical duplicates
Summary
ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. The interplay between histones and DNA serves as an important regulatory point for controlling gene expression. Transcriptionally active elements, such as promoters and enhancers, are defined by short regions of DNA that are devoid of direct histone interactions. These regions of “open” chromatin are usually occupied by transcription factors that facilitate gene transcription. Given the strong correlation between open chromatin and active regulatory elements, this topological feature has become a valuable marker that researchers can use to identify putative promoter and enhancer elements of interest
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