[galaxy-user] LASTZ: Controlling Length of Hits

[Bob Harris]

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