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Old 08-05-2014, 05:47 AM   #1
velt
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Location: Paris

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Default Problem to display wig files on UCSC.

Hello everyone,

Since the arrival of TopHat2 I completely abandoned the use of TopHat1. The problem is that the "Wiggles" tool of TopHat does not exist for TopHat2. (In addition, the Wiggles tool was very slow). So I use IGVtools count, now, to generate my wig files. The problem is that the wig files are displayed in the IGV tool but not in the UCSC genome browser. Yet I have no error when uploading wig files in UCSC. But the data does not appear, the frame corresponding to the file remains empty. I can not find solutions to my problem.

Wig file I use :

Quote:

track type=wiggle_0 name="sample_name" description="description" visibility=full alwaysZero=on windowingFunction=maximum
variableStep chrom=chr1 span=10
14371 1.8
14381 2
14391 2
14401 2
14411 1.8
14891 1
14901 1.6
14911 3.7
14921 5.1
14931 5.8
14941 5
14951 4.4
...
...
...
variableStep chrom=chr10 span=10
96331 1
96341 1
96351 1
96361 1
97191 1
97201 1
97211 1.5
97221 2
97231 2
97241 1
97251 1
97341 2
97351 2.9
...
...
...
Someone used IGVtools to generate these wig files? You encounter this problem?

And if not, what tool you used to generate wig file for RNA-seq data?

Thank you in advance for your help.
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Old 08-05-2014, 06:49 AM   #2
biocomputer
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Quote:
Originally Posted by velt View Post
Yet I have no error when uploading wig files in UCSC. But the data does not appear, the frame corresponding to the file remains empty. I can not find solutions to my problem.
I think this means your upload is timing out. If your file take too long to upload and/or is over 500MB you'll have to convert it to bigwig and put it on a server. In my experience if you're over 500MB you'll get an error message but if it's taking too long you just get the blank screen with no error.
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Old 08-05-2014, 07:14 AM   #3
velt
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Thank you for your reply !
This is not a timeout problem. Indeed, my file weighs only 300 MB.
And even when I split into four equal sized files, and I want to upload these files to UCSC, I have no error and data not be displayed.
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Old 08-05-2014, 09:02 AM   #4
biocomputer
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How long are the files uploading for before you get the error/blank screen? 300MB should be fine as long as your upload speed is fast enough to upload within the required time limit (which is a few minutes I think).
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