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.

Mo Heydarian
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