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. 2019 Nov 4;10:1079. doi: 10.3389/fgene.2019.01079

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Copyright © 2019 Di Filippo, Righelli, Gagliardi, Matarazzo and Angelini

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

PMC Copyright notice

HiCeekR hierarchical data structure. All data are contained in the HiCeekR working directory folder and organized in projects. HiCeekR working directory folder is created the first time HiCeekR is executed, using the configuration file (see Getting Started for the Analysis). Genomes and Annotations can be shared across different projects and are stored in the Genomes and Annotation folders, respectively. All user projects are saved in the specific Project_folder contained in HiCeekR_projects main directory. Within the specific Project_folder it is possible to create sub-folders related to a specific sample, and/or analysis resolution. Each sub-folder contains Results and SysOut folders. Folder Results contains a sub-folder for each analysis step where intermediate and final results are saved. Folder SysOut contains internal logs file and it is not meant for standard users.