ATAC-pipe : general analysis of genome-wide chromatin accessibility
© The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissionsoup.com..
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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2019 |
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| Erschienen: |
2019 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:20 |
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| Enthalten in: |
Briefings in bioinformatics - 20(2019), 5 vom: 27. Sept., Seite 1934-1943 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Zuo, Zuqi [VerfasserIn] |
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| Links: |
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| Themen: |
ATAC |
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| Anmerkungen: |
Date Completed 21.07.2020 Date Revised 21.07.2020 published: Print Citation Status MEDLINE |
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| doi: |
10.1093/bib/bby056 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM286250616 |
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| 520 | |a © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissionsoup.com. | ||
| 520 | |a 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 | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a ATAC | |
| 650 | 4 | |a chromatin accessibility | |
| 650 | 4 | |a regulatory network | |
| 650 | 4 | |a transcription factor | |
| 650 | 7 | |a Chromatin |2 NLM | |
| 700 | 1 | |a Jin, Yonghao |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Wen |e verfasserin |4 aut | |
| 700 | 1 | |a Lu, Yichen |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Bin |e verfasserin |4 aut | |
| 700 | 1 | |a Qu, Kun |e verfasserin |4 aut | |
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