peak2bed
peak2bed converts FindPeaks .peaks output into BED format to represent genomic peak coordinates and associated metadata for downstream analysis and visualization.
Key Features:
- Conversion Capability: Converts FindPeaks .peaks files into BED (.bed) files while preserving peak coordinates and associated metadata.
- Parsing and Data Extraction: Parses .peaks files to extract relevant genomic coordinates and metadata required for BED representation.
- Galaxy Integration: Integrates with the Galaxy execution engine (Galaxy@Pasteur) for execution within workflows on the Institut Pasteur cluster.
Scientific Applications:
- Genomic Data Analysis: Prepares peak data for downstream analyses including motif discovery, differential binding analysis, and integration with other genomic datasets.
- Visualization: Produces BED files suitable for visualization in genome browsers such as UCSC Genome Browser and IGV.
Methodology:
Parses the .peaks file generated by FindPeaks, extracts genomic coordinates and metadata, and formats this information into a BED file.
Topics
Collections
Details
- Maturity:
- Mature
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 12/19/2016
- Last Updated:
- 6/16/2020
Operations
Data Inputs & Outputs
Formatting
Inputs
Outputs
Publications
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research. 2016;44(W1):W3-W10. doi:10.1093/nar/gkw343. PMID:27137889. PMCID:PMC4987906.
Mareuil F, Doppelt-Azeroual O, Ménager H. A public Galaxy platform at Pasteur used as an execution engine for web services. Unknown Journal. 2017. doi:10.7490/f1000research.1114334.1.