EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis.
DNA methylation data analysis
Docker
Galaxy platform
WGBS pipeline
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
02 Apr 2020
02 Apr 2020
Historique:
received:
02
11
2019
accepted:
16
12
2019
entrez:
4
4
2020
pubmed:
4
4
2020
medline:
24
10
2020
Statut:
epublish
Résumé
DNA methylation is a crucial epigenomic mechanism in various biological processes. Using whole-genome bisulfite sequencing (WGBS) technology, methylated cytosine sites can be revealed at the single nucleotide level. However, the WGBS data analysis process is usually complicated and challenging. To alleviate the associated difficulties, we integrated the WGBS data processing steps and downstream analysis into a two-phase approach. First, we set up the required tools in Galaxy and developed workflows to calculate the methylation level from raw WGBS data and generate a methylation status summary, the mtable. This computation environment is wrapped into the Docker container image DocMethyl, which allows users to rapidly deploy an executable environment without tedious software installation and library dependency problems. Next, the mtable files were uploaded to the web server EpiMOLAS_web to link with the gene annotation databases that enable rapid data retrieval and analyses. To our knowledge, the EpiMOLAS framework, consisting of DocMethyl and EpiMOLAS_web, is the first approach to include containerization technology and a web-based system for WGBS data analysis from raw data processing to downstream analysis. EpiMOLAS will help users cope with their WGBS data and also conduct reproducible analyses of publicly available data, thereby gaining insights into the mechanisms underlying complex biological phenomenon. The Galaxy Docker image DocMethyl is available at https://hub.docker.com/r/lsbnb/docmethyl/. EpiMOLAS_web is publicly accessible at http://symbiosis.iis.sinica.edu.tw/epimolas/.
Sections du résumé
BACKGROUND
BACKGROUND
DNA methylation is a crucial epigenomic mechanism in various biological processes. Using whole-genome bisulfite sequencing (WGBS) technology, methylated cytosine sites can be revealed at the single nucleotide level. However, the WGBS data analysis process is usually complicated and challenging.
RESULTS
RESULTS
To alleviate the associated difficulties, we integrated the WGBS data processing steps and downstream analysis into a two-phase approach. First, we set up the required tools in Galaxy and developed workflows to calculate the methylation level from raw WGBS data and generate a methylation status summary, the mtable. This computation environment is wrapped into the Docker container image DocMethyl, which allows users to rapidly deploy an executable environment without tedious software installation and library dependency problems. Next, the mtable files were uploaded to the web server EpiMOLAS_web to link with the gene annotation databases that enable rapid data retrieval and analyses.
CONCLUSION
CONCLUSIONS
To our knowledge, the EpiMOLAS framework, consisting of DocMethyl and EpiMOLAS_web, is the first approach to include containerization technology and a web-based system for WGBS data analysis from raw data processing to downstream analysis. EpiMOLAS will help users cope with their WGBS data and also conduct reproducible analyses of publicly available data, thereby gaining insights into the mechanisms underlying complex biological phenomenon. The Galaxy Docker image DocMethyl is available at https://hub.docker.com/r/lsbnb/docmethyl/. EpiMOLAS_web is publicly accessible at http://symbiosis.iis.sinica.edu.tw/epimolas/.
Identifiants
pubmed: 32241255
doi: 10.1186/s12864-019-6404-8
pii: 10.1186/s12864-019-6404-8
pmc: PMC7114791
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
163Subventions
Organisme : Ministry of Science and Technology, Taiwan (TW)
ID : MOST107-2321-B-002-057
Organisme : Ministry of Science and Technology, Taiwan (TW)
ID : MOST108-2321-B-037-001
Organisme : Institute of Information Science, Academia Sinica
ID : flagship program
Organisme : Institute of Information Science Academia Sinica
ID : flagship program
Organisme : Ministry of Science and Technology, Taiwan
ID : MOST108-2314-B-001-002
Organisme : Ministry of Science and Technology, Taiwan
ID : MOST108-2321-B-038-003
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