Forum: Bad Exprience on bigwig Format Visualization in UCSC
0
gravatar for Shicheng Guo
3.0 years ago by
Shicheng Guo7.4k
Shicheng Guo7.4k wrote:

Just share some disadvantage of bigwig visualization with bigwig. Before bigwig, I usually use bedgraph or wig to show my data with UCSC browser. It is complicated, you need to upload your wig/bedgraph one by one to UCSC. What's worse, the data would be disappeared without visit during 4 month. Therefore, I try to use bigwig to reveal my data. However, new problem is coming:

Generally, It works, however, the performance on large number of bigwig files is exactly very bad.

1, ftp server error on cmd=[] response=[],can't get the data socket: For some tracks, this error were reported since I have two many tracks, in my case, 200 tracks were existed. It seems the FTP server can not support so many connections.

2, Error in TCP non-blocking connection() 111-connection refused, can't get the data socket...Some tracks can not be shown for any reason.

3, Not stable, suppose you have 20 tracks. sometime you can get 10 tracks, sometimes you can get 15 tracks, sometime you can get only 1 tracks to be shown.

What I can say is the usage experience is not very good for bigwig in UCSC browser.

ucsc bigwig forum ftp • 1.4k views
ADD COMMENTlink modified 3.0 years ago by Chris Miller20k • written 3.0 years ago by Shicheng Guo7.4k

Could this be because of your local server/firewall settings messing with connection requests from UCSC? I assume you are serving your files from a local webserver.
@Sukhdeep has a nice tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by genomax65k

You might post feedback on the UCSC Genome Browser discussion group.

ADD REPLYlink written 3.0 years ago by Alex Reynolds28k
2
gravatar for Devon Ryan
3.0 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

I would generally use IGV locally unless you absolutely require a bunch of different UCSC tracks. The performance will be better. You're correct that ftp servers allow a fairly limited number of concurrent connections. At some point you really can't expect remote file access to work very fluidly.

ADD COMMENTlink written 3.0 years ago by Devon Ryan89k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 904 users visited in the last hour