On Mar 21, 2011, at 1:45 PM, JASON G. BANKERT wrote:
We're trying to only get hits of certain lengths. Is there a
setting to use that sets the minimum length for each hit?
Lastz (the underlying program) has some options that are geared toward
filtering by length, though none uses length exactly. In the lastz
wrapper for galaxy, the only length-relevant filtering option is "Do
not report matches that cover less than this percentage of each
read". If your reads are all the same length, or close to the same
length, this could meet your needs. If the length distribution of
your reads is pretty wide (as can occur with 454), then probably not.
I'm not familiar with all the rest of the galaxy toolset, but it seems
like there's bound to be a tool that can compute interval length from
the interval's start and end, and then filter on that.
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