Hello, I have encountered a problem when visualizing my custom Wig tracks. I first noticed that after loading the files, some of the tracks were missing peaks for very long stretched (sometimes an entire arm of a chromosome) while the files themselves do contain the data. After further investigation, I realized that the problematic tracks were those containing very large peaks at near the centromeric boundaries. It appears that when a large peak (>10,000) occurs all the bins to the left and some to the right disappear or are distorted. I have search the site (mainly the WIG Format page) for any guidelines on a maximum number of counts per bin but was unable to find any such information.
Is there a limit to the peak size beyond which the track can no longer be properly visualized? I have prepared an example of the problem I have been experiencing. I have loaded 5 Wig tracks showing my original data and 4 tests in which I gradually decrease the limit on the maximum peak permitted (the data is all the same except that peaks above a certain value are decreased to a set threshold). Test1 does not allow a value above 100,000 , test2 - 50,000, test3 - 25,000, and test4 - 10,000. What I observe is that with each decrease the "real" data is better resolved and less distorted. My Sessions: Example1 shows Chromosome 10 in its entirety (the p-arm is distorted) and Example2 zooms in on a region in the p-arm that shows the problem more clearly. Here is a UCSC browser session I'd like to share with you: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Baghalb&hgS_otherUserSessionName=WigTrack_problem_example1 Here is a UCSC browser session I'd like to share with you: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Baghalb&hgS_otherUserSessionName=WigTrack_problem_example2 Sincere thanks, Basel Baghal _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
