Any recommended way to share ChIP track to collaborator through UCSC browser without using local FTP?

Question

[Pei]

Hello!

My question is: Is there anyway I can generate some URLs to my files and paste them to UCSC genome browser, without using any local FTP server?

My collaborator hope to view the coverage track of our ChIP experiment in UCSC genome browser. At first, I directly submit those bedgraphs to UCSC genome browser but found that after 2 to 3 files the submission begin to fail. I learn that instead, I could provide URL to my file to UCSC genome browser but unfortunately, I do not have a FTP to use. I do not have a linux server, actually.

Is it ok to upload files to Galaxy first and then use the links generate by Galaxy?

Please feel free to let me know if you have any suggestions.

Thank you!

Best,
Patrick

Answer 1

[GenoMax]

Options for hosting files on internet are discussed here: https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html#Hosting

Galaxy could indeed be an option.

[Pei]

Thank you! I'll read this. Are there any example of generating a track using galaxy url?

[GenoMax]

Link above includes a tutorial for that.

[Pei]

Thanks. Now the option of "display at UCSC" appear to be not available on Galaxy. I tried the hub method and it looks good so far. Best,

[GenoMax]

There is build custom track for UCSC tool: https://usegalaxy.org/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fucsc_custom_track%2Fbuild_ucsc_custom_track_1%2F1.0.1&version=latest