sort bedFile.bed | bedItemOverlapCount [options] <database> stdin


This tool is part of UCSC Genome Browser's utilities.

To create a bigWig file from this data to use in a custom track:
sort -k1,1 bedFile.bed | bedItemOverlapCount [options] stdin \
> bedFile.bedGraph
bedGraphToBigWig bedFile.bedGraph chrom.sizes
where the chrom.sizes is obtained with the script: fetchChromSizes
See also:
-zeroadd blocks with zero count, normally these are ommitted
-bed12 expect bed12 and count based on blocks
Without this option, only the first three fields are used.
-max if counts per base overflows set to max (4294967295) instead of exiting
-outBounds output min/max to stderr
-chromSize=sizefile Read chrom sizes from file instead of database
sizefile contains two white space separated fields per line:
chrom name and size
-host=hostname mysql host used to get chrom sizes
-user=username mysql user
-password=password mysql password

* You may want to separate your + and - strand
items before sending into this program as it only looks at
the chrom, start and end columns of the bed file.
* Program requires a connection to lookup chrom sizes for a sanity
check of the incoming data. Even when the -chromSize argument is used
the must be present, but it will not be used.

* The bed file *must* be sorted by chrom
* Maximum count per base is 4294967295. Recompile with new unitSize to increase this

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