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
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.