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?

The short answer is no, but I expect there are other tools in galaxy that could do that filtering.

There are two reasons lastz doesn't provide filtering based on length. First, there are three possible interpretations of what "length" is, all equally valid. Should it be the length of the hit in the reference, or in the read? Or should it be the number of positions in the alignment? Second, even if there is no difference in the three lengths, length is a poorer discriminator than the number of matches. For example, a strict length cutoff of 100 would reject a exact match of length 99 but keep a 90-match-10-mismatch hit.

I'm not familiar enough with galaxy to give you specific details of how to filter by length. But if you choose tabular output from lastz you should be able to use galaxy's "text manipulation" tools to compute the length, then one of the "filter and sort" tools to discard short alignments. Or, if you are using SAM output, it looks like you could use "convert SAM to interval" in the "NGS: SAM Tools" group, then compute the length and filter as above.

Hope that is helpful,
Bob H

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