[Genome] bedgraph data will not display points

[Lionel Brooks]

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

[Hiram Clawson]

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 (Lee) Brooks 3rd]

Hi Hiram,

>From
http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format

1. Pseudo /line graphs/ can be drawn with the wiggle tracks by
setting optional drawing parameters in the display of the track to
draw /points/ instead of bars with smoothing on to smear the
points together into a line.

The pseudo line graph functionality is what I desire.
Previously, it had been possible to do this with bedgraph format files.
I don't know what "smearing" means. I'm just looking for a quick way to
draw the moving average as I had been able to do before.
As I mentioned below, my track line is:

track type=bedGraph autoScale=on graphType=points windowingFunction=mean
smoothingWindow=16

I suppose my solution is to modify my scripts to use the wiggle variable
step format?


thanks,
-Lionel

[Hiram Clawson]

It won't make any difference what type of wiggle format you choose.
They all draw the same way.

You are going to have to provide me with a URL to your data file
so I can see what it looks like.

--Hiram