TrackHub Generator

Generates and updates track hubs for use with the Ensembl Track Hub Registry.

Through advances in instrumentation proteomic analysis generate huge amounts of data for a single sample. In a proteogenomic setting all sequenced peptides then need to be mapped to their respective genomic coordinates to be visualised in a genome browser.

Further information

The script will generate a folder with subfolders and files as required for a track hub. After successful exit of the script the resulting folder may be moved to an openly accessible server (ftp and http enabled) to be able to load the hub in online genome browsers such as the UCSC Genome Browser, the Ensembl Genome Browser and BioDalliance. For more information about track hubs and how to customize the generated hub further please refer to the UCSC TrachHub Infopage.

To run the TrackHubGenerator enter the following command prompt or unix shell:

perl TrackHubGenerator.pl PATH/TO/NAME ASSEMBLY FBED UCSC EMAIL

Positional arguments:

Path to the folder containing the bedTobigBed binary and the fetchChromSizes script previously downloaded from UCSC

PATH/TO/NAME
Path to location where track hub will be created ending with the name for the track hub
ASSEMBLY
Assembly of the genome for which the track hub shall be used, e.g. hg38
FBED
Path to the folder containing all BED files which should be included in the track hub. Each BED file will result in a separate track
UCSC
Path to the folder containing the bedTobigBed binary and the fetchChromSizes script previously downloaded from UCSC
EMAIL
Email address to be used as contact for people using the track hub

Test Examples

Test examples, requirement specifications and time estimations are available here.

Contact

If you need help or have any queries, please contact us using the details below.

Christoph Schlaffner (christoph.schlaffner@sanger.ac.uk)


Sanger Institute Contributors

Previous contributors

Photo of Jyoti Choudhary

Jyoti Choudhary

Former Head of Mass Spectrometry