Hi,<div>I am using the &quot;Count intervals in one file overlapping intervals in another file&quot; 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. </div>
<div><br></div><div>In reading the bedTools manual, it seems like this tool is the &quot;windowBed&quot; 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?</div>
<div><br></div><div>Hopefully this can explain my incorrectly recorded reads.</div><div><br></div><div>Thanks in advance.</div><div><br></div><div><br clear="all">Cheers, <div>Mo Heydarian<br><br></div>
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