You can not mix different span=N numbers. All span specifications need to be identical. It isn't going to function properly as you have it set currently. If Bioconductor is producing this output, it is wrong.
See also: http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format --Hiram Shraddha Pai wrote: > Hi, > I've uploaded a wiggle track for normalized intensity values for an Affy > tiling array. > The track content appears and disappears (ie. I see "no data" and no data) at > different magnifications. > Specifically, I consistently find that the track is present at low mags > (seeing whole chromosome, or one arm), but disappears for windows containing > <100K. > > The file was generated using the Bioconductor package "rtracklayer". I've > pasted track configuration parameters and a snippet from my uploaded data > file below for further information. > > Two related queries: > 1. Incidentally, when I first uploaded the track, I couldn't see anything, no > matter what the zoom level was - simply got a "no data" string by the track > name on the left-hand side. So I made a second wiggle track using example > code from the UCSC wig format page. Sometime when I was playing with the > second sample, the first one suddenly showed the data! > > 2. When the track does display, positive values show in the track colour and > negative values in gray - is this expected behavior too? > > Thanks in advance, > > Shraddha Pai > Post-doctoral fellow, Petronis lab > Centre for Addiction and Mental Health > Toronto, ON > > > > ---- > These are the track configuration options: > track type=wiggle_0 name="latest" description="variableStep format" > visibility=full autoScale=off viewLimits=-3:3 color=50,150,255 yLineMark=0 > yLineOnOff=on priority=10 > ---- > Also, here is a snippet from the top of my uploaded data file: > ---- > track name="latest" type=wiggle_0 > variableStep chrom=chr5 span=19 > 72320 -0.96 > 100685 -1.36 > 105275 0.65 > 137176 0.17 > 216960 -0.04 > 220970 -0.2 > 224750 -0.29 > 256810 0.02 > 265560 -1.25 > 270369 -0.24 > 277861 -1.52 > 332854 -0.75 > 441452 1.91 > 453632 -0.08 > 517466 -1.84 > 526474 0.28 > 611301 -1.61 > 625738 -0.19 > variableStep chrom=chr5 span=20 > 71508 0.51 > 93422 0.8 > 103954 -1.3 > 145392 -0.86 > 150226 -0.41 > 163315 0.79 > 211215 0.5 > 246359 -0.92 > 246469 -0.17 > 249592 0.6 > 269522 -0.98 > 271665 -0.97 > 319299 -0.53 > 333030 -0.22 > 370913 0.89 > 431995 0.59 > 439974 0.23 > 497905 0.79 > 507938 -0.76 > 615494 -1.19 > 625416 0.03 > 627530 -1.4 > <<< > > ______________________________________________________________________ > This email has been scanned by the CAMH Email Security System. > ______________________________________________________________________ > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
