Proteogenomics related formats
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Short talk at the Proteomics Standards Initiative (PSI) meeting in Ghent (April 18-20 2016)
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Proteogenomics related formats
- 1. ProteoGenomics related formats: proBed and proBAM EMBL-EBI Hinxton, Cambridge, UK Dr. Juan Antonio Vizcaíno
- 2. Juan A. Vizcaíno juan@ebi.ac.uk PSI meeting Ghent, 18 April 2016 Proteogenomics related formats • Two ongoing formats are being developed: proBed and proBAM. • Same overall objective: to map identified peptides to genome coordinates. • Different level of detail: • proBed is tab-delimited and simpler, based on the original BED format. Less level of detail. • proBAM is based in the original SAM/BAM formats, widely used in genomics. Much higher level of detail.
- 3. Juan A. Vizcaíno juan@ebi.ac.uk PSI meeting Ghent, 18 April 2016 Proteogenomics related formats
- 4. Juan A. Vizcaíno juan@ebi.ac.uk PSI meeting Ghent, 18 April 2016 proBed files 12 Mandatory columns, 12 optional columns • Tab delimited format, that extends the original BED format (developed by UCSC). • The 12 original fields are unchanged from the original BED. • Additional 12 fields extend the format for reporting PSMs. • It can be converted to the binary indexed version (bigBed) with the available Bed tools. • It needs to be compatible with Bed tools. • bigBed is a format supported by genome browsers to provide external annotations as ‘TrackHubs’.
- 5. Juan A. Vizcaíno juan@ebi.ac.uk PSI meeting Ghent, 18 April 2016 proBed file format specification • Status: format is “final”. • Final example files to be generated. • Not sure whether it is worth going through the PSI standardisation process
- 6. Juan A. Vizcaíno juan@ebi.ac.uk PSI meeting Ghent, 18 April 2016 proBAM format (X. Wang, G. Menschaert) • Supported used cases: • Includes the exact positions of the origin of a peptide identification in the genome • Includes very detailed information related to proteomics data • Serving as a well-defined interface between PSM identification and downstream analyses • The Sequence Alignment Map format (SAM/BAM) • BAM-a highly integrated and compact structure to describe genomic alignments. – Flexible in style – A well defined interface between alignment and downstream analyses – Compact in size – Efficient in random access or integration
- 7. Juan A. Vizcaíno juan@ebi.ac.uk PSI meeting Ghent, 18 April 2016 proBAM file specification • Status: closed to finish the first phase (development by a small group). To be circulated to PSI mailing list. • The format is much more detailed that proBed. • First tools to produce the software exist. • Going to be submitted to the PSI standardisation process.
- 8. Juan A. Vizcaíno juan@ebi.ac.uk PSI meeting Ghent, 18 April 2016 proBAM file specification
- 9. Juan A. Vizcaíno juan@ebi.ac.uk PSI meeting Ghent, 18 April 2016 Provide your own data to genome browsers
- 10. Juan A. Vizcaíno juan@ebi.ac.uk PSI meeting Ghent, 18 April 2016 TrackHubs in Ensembl
- 11. Juan A. Vizcaíno juan@ebi.ac.uk PSI meeting Ghent, 18 April 2016
- 12. Juan A. Vizcaíno juan@ebi.ac.uk PSI meeting Ghent, 18 April 2016
- 13. Juan A. Vizcaíno juan@ebi.ac.uk PSI meeting Ghent, 18 April 2016 Acknowledgements proBED Andy Jones Tobias Ternent Fawaz Ghali proBAM X. Wang G. Menschaert E. Deutsch BBSRC PROCESS grant BBSRC ProteoGenomics grant Ensembl team at EMBL-EBI: A. Yates, A. Vullo & P. Flicek