We are analyzing https://link.springer.com/article/10.1186/s12864-018-4559-3.

Title:
ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data | BMC Genomics
Description:
Background 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. 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. Results We 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. Conclusions This 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 .
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Keywords {🔍}

atacseq, pubmed, quality, reads, article, chromatin, package, google, scholar, atacseqqc, sequencing, size, analysis, library, data, srr, fragments, central, regions, distribution, read, cas, fig, function, assessment, datasets, file, plots, additional, tsss, libraries, open, dna, nucleosomefree, accessibility, cell, results, genome, depth, bam, studies, signals, full, methods, aligned, dataset, cells, number, nucleosome, diagnostic,

Topics {✒️}

org/packages/release/bioc/html/biostrings org/packages/release/bioc/html/motifdb org/packages/release/bioc/html/rsamtools org/packages/release/bioc/html/atacseqqc ataqc/atac-seq/dnase-seq pipelines org/packages/release/bioc/html/bsgenome profile chromatin states lihua julie zhu atac-seq/dnase-seq pipeline [14] low-quality atac-seq experiments gene-centric view successful atac-seq assay article download pdf successful atac-seq experiments fans-assisted atac-seq haibo liu representative atac-seq datasets representative atac-seq libraries submitted atac-seq dataset atac-seq-specific qa successful atac-seq experiment atac-seq library srr89127 perform atac-seq experiments atac-seq fragments shorter house atac-seq experiments post-alignment quality assessment atac-seq library quality public atac-seq datasets aligned atac-seq data aligned atac-seq datasets assaying chromatin accessibility sequence alignment/map format ideal atac-seq dataset detailed view detailed quality control increased background signals open chromatin state dnase-seq processing pipeline article ou fast gapped-read alignment quality control steps oligo-nucleosome-occupied fragments transposed atac-seq library high-resolution technique optimal atac-seq libraries oligo-nucleosome-bound regions transposed atac-seq assays quality control performed assess chromatin accessibility inferred nucleosome-free fragments

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WebPage:
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         description: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. 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. We 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. This 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 .
         datePublished:2018-03-01T00:00:00Z
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            Plant Genetics and Genomics
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      headline:ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data
      description: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. 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. We 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. This 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 .
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      dateModified:2018-03-01T00:00:00Z
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         ATAC-seq
         Quality control
         ATACseqQC
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         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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      name:Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, USA
      name:Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, USA
      name:Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, USA
      name:Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, USA
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