Question: Problem viewing a bigWig file on UCSC browser - any debugging solutions?
gravatar for Ian
3.0 years ago by
University of Manchester, UK
Ian5.4k wrote:

I create a lot of bigWig files from the output of MACS2 to view on the UCSC genome browser. But occasionally I get a bigWig file that has problems.

The problem manifests as when certain areas of the genome are zoomed in the server/browser connection times out. Whole chromosomes can be viewed, but below a certain resolution the time out error occurs.

I have tried recreating the bigWig files, but the "same" output is generated (as determined by md5sum). I do not know where the problem lies.

Has anyone found/developed a way to "debug" a faulty bigWig file?


ucsc bigwig • 1.2k views
ADD COMMENTlink written 3.0 years ago by Ian5.4k

I suspect I'm one of the few people on this side of the pond that can debug bigWig files. You might install pyBigWig and see if you can open/query the file with that. The most likely cause for failures on remote files is a network time out. Alternatively, perhaps you somehow created a bigWig file with poorly chosen "zoom levels", in which case the genome browser would probably just break once you zoom in past a certain point.

Do you have similar problems if you use IGV on the files? How did you create the bigWig files?

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Devon Ryan90k

I will give pyBigWig a go. The file can be viewed in IGV using coordinates that break the UCSC browser. The .bdg file from MACS2 was sent to bedClip and then bedGraphToBigWig. Is it possible to change the zoom levels with pyBigWig?

ADD REPLYlink written 3.0 years ago by Ian5.4k

Sort of, you can set the number of zoom levels, which will then change their size. The maximum number of zoom levels in bedGraphToBigWig is 10, so that's what pyBigWig defaults to. You can change that while making a new bigWig file with the addHeader() command, which takes an optional maxZooms option.

BTW, don't ever make a bigWig file that lacks zoom levels unless you don't want to ever use it in any genome browser.

ADD REPLYlink written 3.0 years ago by Devon Ryan90k

Maybe the issue has nothing to do with the file itself?!? Have you tried another bigWig file (something like a 'positive control') to see if it gets attached fine even when you zoom in? It may be worth attaching your bigWig to another browser as well to see if the problem gets replicated. Try to upload it to the Ensembl Browser to double check that. This tutorial gives more info.

ADD REPLYlink written 3.0 years ago by Denise - Open Targets4.9k

When the offending track is removed from the session there is no longer a problem zooming. The corresponding input sample bigWig does not cause any problems in the same session.

ADD REPLYlink written 3.0 years ago by Ian5.4k
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