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• W2980454008 abstract "Abstract Assay of Transposase-Accessible Chromatin by deep sequencing (ATAC-seq) has been widely used to profile the chromatin accessibility genome-wide. For the absence of an integrated scheme for deep data mining of specific biological issues, here we present ATAC-pipe, an efficient pipeline for general analysis of chromatin accessibility data obtained from ATAC-seq experiments. ATAC-pipe captures information includes not only the quality of original data and genome-wide chromatin accessibility but also signatures of significant differential peaks, transcription factor (TF) occupancy and nucleosome positions around regulatory sites. In addition, ATAC-pipe automatically converts statistic results into intuitive plots at publication quality, such as the read length distribution, heatmaps of sample clustering and cell-type-specific regulatory elements, enriched TF occupancy with motifs footprints and TF-driven regulatory networks. ATAC-pipe provides convenient workflow for researchers to study chromatin accessibility and gene regulation. Availability https://github.com/QuKunLab/ATAC-pipe" @default.
• W2980454008 created "2019-10-25" @default.
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• W2980454008 date "2019-06-11" @default.
• W2980454008 modified "2023-10-18" @default.
• W2980454008 title "ATAC-pipe: general analysis of genome-wide chromatin accessibility" @default.
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• W2980454008 doi "https://doi.org/10.1093/bib/bby056" @default.
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