How To Keep Up The Genome Browser Session Continuously

Question

[Hamilton]

Hi Folks,

I generated a genome browser session with my chip-seq data for a specific chr region with high significant peak score. btw i would like to keep this session. The file does not work after for a while (probably after a few of days)

how can i keep such a genome browser session as a file?

Thx.

[David Langenberger]

What genome browser are you talking about?

Answer 1

[Gjain]

Hi,

As you have mentioned the genome browser, I am assuming its UCSC genome browser.

In that case, you need to create an account on the UCSC genome broswer, which is free. After that, all the sessions you save will be there.

You will find all your saved sessions here once you log in.

Answer 2

[Mary]

Just so you'll know: you shouldn't consider "sessions" to be archival and forever. One time there was an earthquake and a server got lost. But that's not so common. But in the case of normal use, they can periodically clean out the sessions.

http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html

Saved sessions persist for four months after the last access, unless deleted.

So if you haven't touched it in a while you might come back and see that it's been cleaned out. You should always have your stuff in a custom track that you can re-upload as a backup.

Answer 3

[Sven]

One way to do it would be by not uploading the data set to the UCSC browser, then the session stays intact because the data never gets cleaned out. The way we do this is by generating the UCSC-indexed data as a BigWig file, which is kept on our server, and only uploading the URL to this file to the UCSC browser, which then uses this URL to request the data in the window we are trying to visualize from our server.

We do this with our in-house HOMER package(http://biowhat.ucsd.edu/homer/ ), and a description on how to do this with HOMER can be found here: http://biowhat.ucsd.edu/homer/ngs/ucsc.html . Unfortunately, this requires you to install the HOMER package (which isn't that bad, but requires a little bit of UNIX savviness), but there surely are other ways to make BigWig files... .