Why Some People Prefer To Use Ucsc Browser Instead Of Some Standalone Ones (Like Igb, Gbrowser...)

Question

[9606]

Hi all,

looking at how some biologists / bioinfomaticians work I have noticed that lot of them, even to visualize their own data, use UCSC browser.

I mean, when they have some ".bigWig", ".bed", etc.. files on their local computer, they prefer to upload those files to UCSC and use the online web interface to visualize them, through the Web Browser (FireFox, Chrome, IE, etc...).

I think that the same visualization could be achived by the means of "stand alone" Genome Browsers (among them maybe IGB is the most famous).

1. Am I right if I say that the two tools are equivalent?
2. Why is UCSC soo much used even to visualize local data?

Thank you,

Best Regards.

Answer 1

[Giovanni M Dall'Olio]

The advantage of using a remote UCSC browser is that you can compare your data with other annotations hosted there. On a local browser, you would be forced to download a lot of data to your computer, just to visualize it.

Pros of using remote UCSC browsers:

• you can access a lot of tracks without having to download them
• similarly, all the tracks and the user interface are always up-to-date
• the browser is available from any computer, without having to install it. It's like gmail vs thunderbird.

Answer 2

[Ryan Dale]

Two major advantages for me are UCSC's track hubs and sessions.

Track hubs allow lots of custom filtering and configuration of your data (say, a collection of ChIP-seq experiments with many antibodies, cell types, and a few different peak-calling params). For example, the ENCODE TF track hub has this giant "switchboard" of celltypes and antibodies, with additional filtering below. I don't know of any other browser with this sort of flexibility, though it's possible I haven't dug deep enough.

Sessions are great for collaboration. After setting up a track hub and configuring the view with tracks appropriate to the experiment, I can just send a link to collaborators -- and they see exactly what's on my screen.

Answer 3

[lh3]

IGB and IGV support DAS/1. They can request data in a small region without downloading everything. This way is actually more flexible - for example you can get every Ensembl track on their DAS/1. On the other hand, I have to admit that I have never used DAS resources in IGV. I have just tried IGB. While it loads the track, I do not know how to display them properly in a minute.

I would say UCSC is preferred over IGB etc. because of its simple and clear user interface (UI). The multiple ways of displaying data (e.g. packed, squash, etc.) are very helpful to display complex tracks. I think it should be possible, in principle, to implement such UI in IGB, but that would need tens of man years at least. To this end, I would say the better user experience, but not the data availability, is the key reason that most prefer UCSC.

[Pascal]

+1 for mentioning the UI. I this is exactly the reason I am using UCSC's genome browser. Displaying more than ~10 tracks in UCSC is no problem, while I completely lose overview in IGV.