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.
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written
by
Shicheng Guo
1 answer
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.
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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]
You might post feedback on the UCSC Genome Browser discussion group.