question about the track hub specification

[Electra Tapanari.]

Hi there,

I am creating track hubs and I would to ask you something.

In the UCSC specifications it's mentioned here:

  What Are Track Hubs?

	Track hubs are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser (please note that hosting hub files on HTTP tends to work even better than FTP and local hubs can be displayed on GBiB).

When you say that the hub files are better to be hosted in an HTTP server do you mean the alignment files, ie the CRAM files in my case or the actual flat files and directories of the track hub (hub.txt, genomes.txt etc)

Because in my case the CRAM files are in a different location to the flat track hub files so I would like to know which ones are recommended to be in an HTTP server.

Many thanks in advance,
Electra Tapanari

Ensembl Genomes
European Bioinformatics Institute
Cambridge, UK

[Luvina Guruvadoo]

Hello Electra,

Thank you for your question. We encourage the use of HTTP over FTP simply because FTP is an older system. In terms of performance, the hub.txt and genome.txt files use a relatively small amount of data and are used less intensively. Large files such as bigWig, etc should be mounted on HTTP for better performance.

Also note, hub support for CRAM has not yet been released. It will be a few weeks before this feature is available on our public site.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Regards,

Luvina

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

[Electra Tapanari.]

Hi Luvina,

Thanks so much for your answer.

Best regards,
Electra