greenPipes：一个用于 greenCUT&RUN 和 CUT&RUN 基因组定位数据集的集成数据分析管道。

greenPipes: an integrated data analysis pipeline for greenCUT&RUN and CUT&RUN genome-localization datasets.

机构信息

Department of Urology, Medical Center-University of Freiburg, Freiburg, 79016, Germany.

German Cancer Consortium (DKTK), partnersite Freiburg, a partnership between the DKFZ and Medical Center-University of Freiburg, Germany.

出版信息

Bioinformatics. 2024 May 2;40(5). doi: 10.1093/bioinformatics/btae307.

DOI:10.1093/bioinformatics/btae307

PMID:38718209

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11112040/

Abstract

MOTIVATION

To study gene regulation through transcription factors and chromatin modifiers, a variety of genome-wide techniques are used. Recently, CUT&RUN-based technologies have become popular, but a pipeline for the comprehensive analysis of CUT&RUN datasets is currently lacking. Here, we present the "greenPipes" package, which includes fine-tuned parameters specifically for bioinformatic analyses of greenCUT&RUN and CUT&RUN datasets. greenPipes provides additional functionalities for data analysis and data integration with other -omics technologies, which are either not available in other pipelines developed for CUT&RUN datasets or scattered in the literature as individual packages.

AVAILABILITY AND IMPLEMENTATION

Source code and a manual of the greenPipes are freely available on GitHub website (https://github.com/snizam001/greenPipes). The test datasets, comprehensive annotation files, and other datasets are available at https://osf.io/ruhj9/.

CONTACT

n.sheikh@dkfz-heidelberg.de or m.timmers@dkfz-heidelberg.de.

SUPPLEMENTARY INFORMATION

The handbook of greenPipes is available online at Bioinformatics as Supplementary text.

摘要

动机

为了通过转录因子和染色质修饰物研究基因调控，使用了多种全基因组技术。最近，基于 CUT&RUN 的技术变得流行起来，但目前缺乏用于全面分析 CUT&RUN 数据集的流水线。在这里，我们介绍了“greenPipes”包，它包括专门针对 greenCUT&RUN 和 CUT&RUN 数据集的生物信息学分析的微调参数。greenPipes 提供了其他功能，用于数据分析和与其他 -omics 技术的数据集成，这些功能在为 CUT&RUN 数据集开发的其他管道中不可用，或者在文献中作为单独的软件包分散存在。