Hi Tyler,
I assume you are talking about the bedItemOverlapCount utility. The
utility is in the Genome Browser source tree, and instructions for
downloading the source are here:
http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads
Most of the utilities will print a usage statement when run with no
arguments. Here is the usage statement for bedItemOverlapCount:
---------------------------------------------------------------
$ bedItemOverlapCount
bedItemOverlapCount - count number of times a base is overlapped by the
items in a bed file. Output is bedGraph 4 to stdout.
usage:
sort bedFile.bed | bedItemOverlapCount [options] <database> stdin
To create a bigWig file from this data to use in a custom track:
sort bedFile.bed | bedItemOverlapCount [options] <database> stdin \
> bedFile.bedGraph
bedGraphToBigWig bedFile.bedGraph chrom.sizes bedFile.bw
where the chrom.sizes is obtained with the script: fetchChromSizes
See also:
http://genome-test.cse.ucsc.edu/~kent/src/unzipped/utils/userApps/fetchChromSizes
options:
-zero add 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
Notes:
* 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 <database> connection to lookup chrom sizes for a
sanity
check of the incoming data. Even when the -chromSize argument is used
the <database> 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
---------------------------------------------------------------
I hope this helps. If you have further questions, please feel free to
contact us again at [email protected].
--
Brooke Rhead
UCSC Genome Bioinformatics Group
On 08/18/10 07:19, TYLER MALYS wrote:
> Hi,
>
> I'm a grad student at Penn State University. I'm currently working with
> several chip-seq data tracks from you browser. I'm trying to understand how
> the wiggle tracks for the Hudson Alpha and Yale transcription factor binding
> tracks are assembled as well as how the Broad hi stone wiggle tracks are
> assembled. The Bed overlap count utility seems to be used in assembling the
> hudson tracks but I can not find information about how it works. Can you help
> me in these matters.
>
> Thanks
> Tyker
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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