Good Evening Charlie: Your file is very confusing. I can not make much sense of what it should mean.
Your variableStep lines have multiple 'span=nnnn' specifications. Not only do you have multiple 'span' specified in your file, but you have 2,757 different spans specified, from 1 to 3980. The 'span' of a data point means how many bases that data value covers. It is something like the 'width' of each data point. You need to have a single 'span' for all data points. Try getting rid of all the 'span=nnn' specifications on your variableStep declarations lines. They way each data point will occupy a single base. You also have some very unusual fixedStep specifications in your file. For example: fixedStep chrom=chr1 start=8022581 step=0 span=2332 fixedStep chrom=chr1 start=176403643 step=0 span=2356 fixedStep chrom=chr1 start=62054148 step=130450524 span=2373 fixedStep chrom=chr1 start=176537392 step=0 span=2374 fixedStep chrom=chr1 start=169504674 step=0 span=2381 fixedStep chrom=chr1 start=73240457 step=39675763 span=2389 fixedStep chrom=chr1 start=118548936 step=75982211 span=2396 fixedStep chrom=chr1 start=94391174 step=47826275 span=2397 fixedStep chrom=chr1 start=34548878 step=52617155 span=2398 fixedStep chrom=chr1 start=26912866 step=156446543 span=2402 fixedStep chrom=chr1 start=66235309 step=0 span=2404 These specifications do not make much sense. This data doesn't create a graph. Do you know what the graph your data should look like ? --Hiram Chen-Yi (Charlie) Chen wrote: > Hi UCSC genome browser's technical group, > I am Charlie and I recently used UCSC genome browser to try to visualize > our ChIP sequencing data, and then I've encountered some problems. We used > the ht-seq R package that developed by UC Riverside to do the analysis, > and then output the analysis to a WIG file output. By carefully going > through the WIG file format the UCSC genome browser supports, I think the > output WIG file we have is supported by the browser. However, when I > uploaded the this WIG file to custom track, it doesn't show out any peaks > on the genome browser, even though the "score" is in the WIG file. > > Interestingly, when I excerpt part of my WIG file (ex. I excerpt first > 10,000 line), then the peaks display just fine. > > The following address is our WIG files: > full file: > http://radbio.lbl.gov:8080/ChIP/input_chr1.wig > excerpt file: > http://radbio.lbl.gov:8080/ChIP/input_chr1_part.wig > > Our WIG file is generated from the output of ht-seq package (in R) > analysis, and the raw data is aligned by Bowtie with UCSC reference genome > of hg18. > > Thanks for your help! > > -Charlie- > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
