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Old 04-08-2010, 06:26 AM   #3
Thomas Doktor
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Location: University of Southern Denmark (SDU), Denmark

Join Date: Apr 2009
Posts: 105
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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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