Hi Pauline, Thanks for the response. What about the first example I sent: [mt269@swiftgen results]$ cat test.wig fixedStep chrom=chr1 start=1 step=2 0.1 [mt269@swiftgen results]$ wigToBigWig test.wig hg19_chrom_sizes.txt test.bw [mt269@swiftgen results]$ bigWigToWig test.bw /dev/stdout fixedStep chrom=chr1 start=1 step=2 span=2 0.1
Here, the span in the original file should be 1, since it isn't specified, but after running wigToBigWig and bigWigToWig, the span is 2. This seems like incorrect behavior to me. The second example I sent was over-simplified, but I think it makes sense. Why would the step sizes have to be equal? Say I have wig values at positions 1,3,5,7, 8, and 12 each with a span of 1. There is no data at positions 2,4,6,9,10,11. I have code which turns this into a fixedStep wig file as follows: fixedStep chrom=1 start=1 step=2 pos1Val pos3Val pos5Val pos7Val fixedStep chrom=1 start=8 step=4 pos8Val pos12Val If I do this, wigToBigWig throws an error and complains that there is more than one value for position 8. It seems to be doing this because it assumes the span is 2, rather than the default of 1, which doesn't make sense to me. Thanks, Melissa On Thu, Apr 19, 2012 at 6:40 PM, Pauline Fujita <[email protected]> wrote: > Hello Melissa, > > Looking at your input: > > > fixedStep chrom=chr1 start=1 step=2 > > 0.1 > > fixedStep chrom=chr1 start=2 step=1 > > 0.2 > > > the step sizes must be equal for the input to make sense. If I set step=1 on > both lines this runs and returns the same output but with span=1 as > advertised. > > Hopefully this information was helpful and answers your question. If you > have further questions or require clarification feel free to contact the > mailing list at [email protected]. > > Regards, > > Pauline Fujita > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > > On 4/17/12 10:53 AM, Melissa Jane Hubisz wrote: > > Hi UCSC, > I ran into a behavior with wigToBigWig that seems like a bug. If a > span is not specified in fixedStep wig format, it assumes that the > span is the same as the step, rather than the documented default of 1: > > [mt269@swiftgen results]$ cat test.wig > fixedStep chrom=chr1 start=1 step=2 > 0.1 > [mt269@swiftgen results]$ wigToBigWig test.wig hg19_chrom_sizes.txt test.bw > [mt269@swiftgen results]$ bigWigToWig test.bw /dev/stdout > fixedStep chrom=chr1 start=1 step=2 span=2 > 0.1 > > This is the situation that initially caused problems for me: > [mt269@swiftgen results]$ cat test2.wig > fixedStep chrom=chr1 start=1 step=2 > 0.1 > fixedStep chrom=chr1 start=2 step=1 > 0.2 > [mt269@swiftgen results]$ wigToBigWig test2.wig hg19_chrom_sizes.txt > test2.bw > There's more than one value for chr1 base 2 (in coordinates that start with > 1). > > If I manually set span=1 in my files it works OK (i think). Is this a > bug, or am I once again plagued by a mis-understanding of wig > coordinates? > Thanks, > Melissa > _______________________________________________ > Genome-mirror mailing list > [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome-mirror _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
