Good Evening Michael: The error message means that your data points are overlapping each other. 'There's more than one value for chr1 base 40730 (in coordinates that start with 1).'
Your definition line clearly indicates all of your data values will overlap. A span of 300 means that each data point "spans" or covers 300 bases in the genome. One data point will make a bar graph at that value covering 300 bases of the genome. Your step size of 30 means that each new data point starts at 30 bases past the previous data value. Hence, all your data points are overlapping each other. The submission of the ascii wiggle data to the genome browser will not detect this as an error. It will truncate your spans of 300 and simply start the next value at 30 bases past the previous value. The wigToBigWig program will not allow these types of definitions. You may want to reconsider what you are using step and span for and where you want your values to appear and how many bases they should cover. See also: http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format --Hiram ----- Original Message ----- From: "Michael Mccarthy" <[email protected]> To: [email protected] Sent: Saturday, October 22, 2011 5:43:01 AM Subject: [Genome] wigToBigWig (There's more than one value for chr1 base 40730 (in coordinates that start with 1)) Dear UCSC Genomics, I've been trying to convert a ~195MB fixedStep wig file to bigwig, using wigToBigWig, but keep coming up with this error: 'There's more than one value for chr1 base 40730 (in coordinates that start with 1).' For my fixedStep files, I'm using the following header: fixedStep chrom=chr1 start=10010 step=30 span=300. The data is continuous for each chromosome, ie every step along the chromosome has a score of >= 0, without exceeding the length of the chromosome. When I load the data for a single chromosome, or a group of chromosomes in wig format directly to the UCSC browser, the data is displayed correctly, and matches my pile-up track perfectly. When I try to convert a single chromosome wig file to bigWig, I get the same error. When I look at my data around the base position that is called as being in error, it is typically in an area with scores of many 0's either side, but seems to me otherwise unremarkable. It isn't occurring near a fixedStep title line. I've tried adjusting my bin sizes and span sizes, my start positions etc, but to no avail. I don't fully understand exactly what the error means, which makes it much more difficult to fix! If anyone could explain what causes this type of error, I would be very grateful! Thanks in advance, Michael McCarthy, Wellcome Trust Centre for Cellular and Molecular Physiology, University of Oxford, UK _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
