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Old 04-07-2010, 08:16 AM   #1
chrisbala
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Default converting tophat .wig to bigwig for upload into ucsc

Hi,

I'm trying to get my wig file output from tophat into ucsc.

in the past i've had no trouble because my files were small enough. now i am trying to convert into bigwig using UCSCs tools (bedGraphtoBigWig). Unfortunately, I'm getting an error when I do this:

line 10544021 of coverage_familiar_new.wig: start and end coordinates the same
They need to be at least one apart

Is this a problem with how tophat is writing the file? or a problem with the conversion utility? or a problem with me?

thanks!

Chris
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Old 04-07-2010, 08:19 AM   #2
chrisbala
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Default wigtobigwig

i should also say that i tried using wigtobigwig to convert and that did not throw any errors. but I subsequently had errors when I tried to upload to ucsc:

Couldn't zUncompress 3726 bytes: zlib data error
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Old 04-08-2010, 05:26 AM   #3
Thomas Doktor
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I imagine it's the last line of the file describing the coverage of the mitochondrial chromosome which is probably 0, so TopHat reports the start and end coordinates as being both 0. If this is the case, just remove the last line.

Btw, you are correct that the .wig file produced by TopHat is in fact a bedGraph file and should be converted to a bigWig using the bedGraphtobigWig tool.
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Old 04-08-2010, 12:57 PM   #4
chrisbala
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Default start and end are the same

sadly, that does not seem be the case. the line in question is:

chr2_random 1789194 1789194 1

think that such a line exists is a problem? (and if so, how big?)
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Old 04-09-2010, 08:10 AM   #5
Thomas Doktor
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Are there any other lines referring to chr2_random? If not, I would simply remove the line in question as it is likely not of biological importance to your experiment.
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