upload custom tracks with filezilla

[Gema Sanz Santos]

Hello,

 

I´m trying to upload a custom track (bigwig file) to Genome Browser but I´m unable. I have my own Filezilla server but I´m not sure how to write the ftp address (track line). I already tried track: type=bigwig bigDataUrl=ftp:// //ip address/file.bigwig but is not working.

 

Any suggestions? Do I need to open any port for UCSC?

 

Best

Gema

 

 

Gema Sanz Santos, PhD

MTC | Karolinska Institute

Nobelsväg 16

171 77 Stockholm

Room H564

 

[Jonathan Casper]

Hello Gema,

Thank you for your question about uploading a custom track from your own FTP server. Details about how to configure your FTP server will depend on your particular system setup, and fall outside the scope of this mailing list. That said, a good place to begin would be to connect to your own FTP server and see where file.bigWig is located. Is it in the root directory of your FTP server or is it in a subdirectory? If the file is in a subdirectory, you will need to provide that path in the URL. As for ports, the standard port to open for FTP is port 22 - the UCSC Genome Browser will attempt to connect to that port by default for an FTP connection. If you would like to open a different port for FTP, you will need to make sure that port is open for access by the UCSC Genome Browser and describe it in your URL as follows:

ftp://hostname:port/path/to/file.bigWig

One final note - this all assumes that your FTP server is configured to allow anonymous access (with no login credentials). If you use a username and password to connect to your FTP server, you will also need to supply those in the URL in the following format:

ftp://username:password@hostname/path/to/file.bigWig

More information about constructing URLs like this is available on our Custom Tracks documentation at https://genome.ucsc.edu/goldenPath/help/customTrack.html#SHARE. Please note that passwords included in URLs are not protected or encrypted.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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