ArticleNucleic acids research2018
Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
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- Exploring intrinsic variability between cultured nasal and bronchial epithelia in cystic fibrosis.Scientific reports · 2023Article
- Identification of BBX gene family and its function in the regulation of microtuber formation in yam.BMC genomics · 2023Article
- Identification of hub genes and potential ceRNA networks of diabetic cardiomyopathy.Scientific reports · 2023Article
- Genome-wide characterization and expression analysis of the HAK gene family in response to abiotic stresses in Medicago.BMC genomics · 2022Article
- Molecular characteristics of global β-lactamase-producing Enterobacter cloacae by genomic analysis.BMC microbiology · 2022Article
- Next-Generation Sequencing Applications for the Study of Fungal Pathogens.Microorganisms · 2022Review
- MicroRNA-769-3p Acts as a Prognostic Factor in Oral Squamous Cell Cancer by Modulating Stromal Genes.Cancers · 2022Article
- Mettl3-mediated mRNA mNature communications · 2022Article
- Identification and Characterization of Abiotic Stress-Responsive NF-YB Family Genes inInternational journal of molecular sciences · 2022Article
- Bibliometric review of ATAC-Seq and its application in gene expression.Briefings in bioinformatics · 2022Review
- Epidemiological and genomic characteristics of globalFrontiers in microbiology · 2022Article
- Genome Structural Variation Landscape and Its Selection Signatures in the Fast-growing Strains of the Pacific Oyster, Crassostrea gigas.Marine biotechnology (New York, N.Y.) · 2021Article
- BRCA1-BARD1 regulates transcription through modulating topoisomerase IIβ.Open biology · 2021Article
- CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells.Nature cell biology · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.