Good Morning Lionel:
The bedGraph drawing mechanism can construct bar graphs at your
specified intervals, or when you select graphType=points it will
draw only the top of the bar graph at your specified intervals.
There is no line drawing except by the trick of "smoothing" points
such that they appear to be in a line graph. This only works if
the data points are continuous when seen in the genome browser.
Smoothing will not smear points into areas where there is no
data value specified.
The Genome Graphs function of the genome browser:
http://genome.ucsc.edu/cgi-bin/hgGenome
will only draw lines between your specified points.
See also:
http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format
--Hiram
Lionel Brooks wrote:
> Hello all,
>
> I have a bedgraph file. In the past I have used to files to attain
> graphic output in the form of a smoothed line but I uploaded my most
> recent data set and now I cannot get a line graph. In fact, I'm not
> sure what I am looking at because the values that are displayed along
> the y-axis are not described with a label.
>
> Here is my track line:
> track type=bedGraph autoScale=on graphType=points windowingFunction=mean
> smoothingWindow=16
>
> My data format is
>
> chr coordA coordB value
>
> Where approximate distribution of data values are : 5 <= value <= 500.
> Is it possible that your plotting function cannot compute this line
> because my coordinate intervals are too small?
> Another possibly relevant issue may be that the coordinate intervals are
> not fixed length.
>
> Any suggestions for course of action would be great.
>
> Sincerely,
> Lionel
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