Journal
BRIEFINGS IN BIOINFORMATICS
Volume 20, Issue 5, Pages 1934-1943Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bby056
Keywords
ATAC; chromatin accessibility; transcription factor; regulatory network
Funding
- National Natural Science Foundation of China [91640113, 31771428]
- National Key RAMP
- D Program of China [2017YFA0102903]
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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.
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