Hi Hiram, Our wig file is actually output from a R statistics package called ht-seq developed by UC Riverside. I believed the reason why our wig file has so many variableStep and fixedStep is due to the way ht-seq handles these information, and it sort of make sense why it output those files.
After getting rid of all fixedStep entries and eliminate variableStep to only one entry, the peak display seems to work. I still need to consult with my co-worker to see if this result makes sense or not. Thanks! Lastly, why can't we have multiple variableStep entries in the wig file? I though that's actually another way of representing the data when there is a same number of reads throughout "span" in a certain chromosome position. So it makes sense to me that we can have multiple variablesStep because we might have different length of number of reads. Thanks again for your help! -Charlie- > 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
