issues with converting bed to tdf format

[Lee Sande]

Hi,
I have a bed formatted data that looks like this:
chr1 4427500 4428500 4
chr1 4428500 4429500 9
chr1 4429500 4430500 10
chr1 4430500 4431500 6
chr1 4431500 4432500 2

This data is processed (essentially this data represents the number
of reads in the listed interval).
I am interested in looking at the trend (peaks etc) in the data.
This is a big file (100Mb) and when I load it as is, igv simply shows
flat region throughput the
genome, rather than showing peaks (as indicated by the value given in
the 4th column).
Should I be using the "count" command in igvtools to display the
peaks?
I actually did use that command but it takes very long.

How do I go about converting the bed file so that Igv shows the height
according
to the value given in the 4th column?

thanks

[Lee Sande]

I found a way but I am not sure it is the best way.
I converted the file into wig and then use the toTDF command of
igvtools.

[Jim Robinson]

Lee, this is a "bedgraph" file,  just use the "bedgraph" extension and it should work.   The fourth column of a "bed" file is a string name.   Be sure those are tab-delimited columns,  I can't tell.   

Remember that bed and bedgraph are "zero-based" coordinates (first base is zero),  while wig is "one-based",  when doing converting.  

Jim