[Genome] Standardizing the heights of different tracks

[Kayla Smith]

Hello Steve,

There are two ways to change the browser view you've mentioned.

1.  Click on the blue bar on the left hand side of the track in 
question.   In the list of settings at the top of the track details 
page, set "Data view scaling" to "use vertical viewing range setting". 
  You can also set the "Vertical Viewing Range" to whatever values are 
appropriate.

2.  Since you are running a mirror, you can add some information to the 
trackDb.ra block for the tracks in question.  This information is in the 
README file in the trackDb directory.  I'll paste the relevant part of 
the README here:
------------------------------------------------------------------------------

14. type wig [lower] [upper]
    Continuous value graphing track.
    [lower] - overall lower limit of the data, default 0.0
    [upper] - overall upper limit of the data, default 127.0
    trackDb record options:
       autoScale         on|off               # default is off
       gridDefault       on|off               # default is off (draw 
y=0.0 line)
       maxHeightPixels   max:default:min      # default is 128:128:11
       graphType         bar|points           # default is bar
       viewLimits        lower:upper    # default is from the type line 
limits
       yLineMark         real-value     # default is 0.0
       yLineOnOff        on|off         # default is off (draw 
y=yLineMark line)
       windowingFunction maximum|mean|minimum # default is maximum
       smoothingWindow   off|[2-16]           # default is off
       wigColorBy        <bed table>          # use colors in bed for wiggle
                                              #   in overlapping regions
       spanList          s1,s2,s3...          # list of spans in the 
loaded table                #       you can find the spans by doing:
                 #       "select span from <table> group by span"
                 #       typically spanList is only one:
                 #       spanList 1
                 #       rarely it may be more:
                 #       spanList 1,1000
                 #       special efforts must be made to load extra spans
                 #       into the table for special purposes.

--------------------------------------------------------------------------

I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group



Hi,

Could you please help us on the heights of custom tracks?

We have separate ChIP-sequencing experiments on Arabidopsis, each is 
being represented by a separate track.
The "score" is the coverage by sequencing reads. We need that 5x 
coverage (denoted by a horizontal black line here) would be displayed at 
identical height in each experiment and in each window,
Unfortunately, so far it depends on the maximal coverage at the 
individual  window of the individual track.

See the green scores (H3 Drought) 5x runs very high, but at TM Drought 
(bottom score track with Navy blue) it is about a tenth of the height of 
H3 control.

We need that the same coverage would result in the same height in all 
windows in all experiments. Could you please help us with that?

Thank you so much!

Steve



Steve Ladunga
Professor of Computational Biology
UNL Center for Biotechnology and
Department of Statistics
E204 Beadle Center, University of Nebraska-Lincoln
1901 Vine St., Lincoln, NE 68588-0665
Phone: (402) 472-6074
Fax:      (402) 472-3139
sladunga at unl.edu