Dataset Information

DeepTools: a flexible platform for exploring deep-sequencing data.

ABSTRACT: We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg.de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy.

SUBMITTER: Ramirez F

PROVIDER: S-EPMC4086134 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

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Publications

deepTools: a flexible platform for exploring deep-sequencing data.

Ramírez Fidel F Dündar Friederike F Diehl Sarah S Grüning Björn A BA Manke Thomas T

Nucleic acids research 20140505 Web Server issue

We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. ...[more]

PMID: 24799436

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Project description:Next-generation sequencing (NGS) approaches are commonly used to identify key regulatory networks that drive transcriptional programs. Although these technologies are frequently used in biological studies, NGS data analysis remains a challenging, time-consuming, and often irreproducible process. Therefore, there is a need for a comprehensive and flexible workflow platform that can accelerate data processing and analysis so more time can be spent on functional studies.We have developed an integrative, stand-alone workflow platform, named CIPHER, for the systematic analysis of several commonly used NGS datasets including ChIP-seq, RNA-seq, MNase-seq, DNase-seq, GRO-seq, and ATAC-seq data. CIPHER implements various open source software packages, in-house scripts, and Docker containers to analyze and process single-ended and pair-ended datasets. CIPHER's pipelines conduct extensive quality and contamination control checks, as well as comprehensive downstream analysis. A typical CIPHER workflow includes: (1) raw sequence evaluation, (2) read trimming and adapter removal, (3) read mapping and quality filtering, (4) visualization track generation, and (5) extensive quality control assessment. Furthermore, CIPHER conducts downstream analysis such as: narrow and broad peak calling, peak annotation, and motif identification for ChIP-seq, differential gene expression analysis for RNA-seq, nucleosome positioning for MNase-seq, DNase hypersensitive site mapping, site annotation and motif identification for DNase-seq, analysis of nascent transcription from Global-Run On (GRO-seq) data, and characterization of chromatin accessibility from ATAC-seq datasets. In addition, CIPHER contains an "analysis" mode that completes complex bioinformatics tasks such as enhancer discovery and provides functions to integrate various datasets together.Using public and simulated data, we demonstrate that CIPHER is an efficient and comprehensive workflow platform that can analyze several NGS datasets commonly used in genome biology studies. Additionally, CIPHER's integrative "analysis" mode allows researchers to elicit important biological information from the combined dataset analysis.

Dataset Information

DeepTools: a flexible platform for exploring deep-sequencing data.

Publications

deepTools: a flexible platform for exploring deep-sequencing data.

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