PUBLICATION
Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data
- Authors
- Kim, T., Seo, H.D., Hennighausen, L., Lee, D., Kang, K.
- ID
- ZDB-PUB-180209-9
- Date
- 2018
- Source
- Nucleic acids research 46(9): e53 (Journal)
- Registered Authors
- Hennighausen, Lothar
- Keywords
- none
- MeSH Terms
-
- Animals
- DNA-Binding Proteins/metabolism
- Data Mining
- Epigenesis, Genetic*
- Gene Expression Profiling*
- High-Throughput Nucleotide Sequencing*
- Histones/metabolism
- Mice
- STAT5 Transcription Factor/metabolism
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/metabolism
- Software*
- Workflow
- PubMed
- 29420797 Full text @ Nucleic Acids Res.
Citation
Kim, T., Seo, H.D., Hennighausen, L., Lee, D., Kang, K. (2018) Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data. Nucleic acids research. 46(9):e53.
Abstract
Octopus-toolkit is a stand-alone application for retrieving and processing large sets of next-generation sequencing (NGS) data with a single step. Octopus-toolkit is an automated set-up-and-analysis pipeline utilizing the Aspera, SRA Toolkit, FastQC, Trimmomatic, HISAT2, STAR, Samtools, and HOMER applications. All the applications are installed on the user's computer when the program starts. Upon the installation, it can automatically retrieve original files of various epigenomic and transcriptomic data sets, including ChIP-seq, ATAC-seq, DNase-seq, MeDIP-seq, MNase-seq and RNA-seq, from the gene expression omnibus data repository. The downloaded files can then be sequentially processed to generate BAM and BigWig files, which are used for advanced analyses and visualization. Currently, it can process NGS data from popular model genomes such as, human (Homo sapiens), mouse (Mus musculus), dog (Canis lupus familiaris), plant (Arabidopsis thaliana), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), worm (Caenorhabditis elegans), and budding yeast (Saccharomyces cerevisiae) genomes. With the processed files from Octopus-toolkit, the meta-analysis of various data sets, motif searches for DNA-binding proteins, and the identification of differentially expressed genes and/or protein-binding sites can be easily conducted with few commands by users. Overall, Octopus-toolkit facilitates the systematic and integrative analysis of available epigenomic and transcriptomic NGS big data.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping