[Genome] BLAT minScore help

[Chris Smillie]

Hello,

I have read the BLAT documentation and it seems that the score of an
alignment is calculated (roughly) as follows:

(number matches) - (number mismatches) - (some gap penalty).

I am trying to map 33 bp solexa reads onto a set of contigs, and I was
hoping to filter the results with the minScore option.

With 33 bp reads, it seems that the highest score possible would be 33 (33
matches - 0 mismatches - 0 gaps). However, after experimenting with
different cut-off scores, I have found that this is not the case.

When I use the -minScore=33 option, I still get matches that are only 20 bp
in length. Even more, if I use -minScore=9999999999999, I still manage to
get hits!

This is confusing to me and I feel that I must be doing something wrong. Can
you suggest anything? Thank you,

Chris

P.S. Here is an example of a command that I have tried to use:

../../blatSuite.34/blat -t=dna -q=dna -tileSize=6 -stepSize=6 -minMatch=2
-minScore=99999999999999 -minIdentity=93 -out=pslx ../454LargeContigs.fna
../salmonella.fasta out.pslx

But this still manages to return hits...