Hello Mo,

This tool comes from a repository sourced from the Tool Shed:
http://toolshed.g2.bx.psu.edu/

Search for a tool named "bedtools" with owner "aaronquinlan". You could examine the repository and then the tool wrapper author can be contacted directly with questions about parameters or if you think there is a bug.

Hopefully this helps!

Jen
Galaxy team

On 8/16/12 10:13 AM, Mohammad Heydarian wrote:
Hi,
I am using the "Count intervals in one file overlapping intervals in
another file" tool (part of the bedTools package) to assess the number
of RNA-seq reads that map back to a specific region. (I am using this on
the Galaxy test server). I am finding that this tool returns many more
reads than it should.

In reading the bedTools manual, it seems like this tool is the
"windowBed" tool and it actually has many more parameters that are not
shown on the Galaxy interface. What are these (hidden) settings for
these parameters that are not shown?

Hopefully this can explain my incorrectly recorded reads.

Thanks in advance.


Cheers,
Mo Heydarian



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