[Genome] blat didn't work on 33mers

[Yueming Ding]

Generator Microsoft Word 11 (filtered medium) HI Jim,

I tried to use Blat to align 33mers to mouse genome. But it didn' t work. I blatted 725000 33mers. After I ran pslReps, I only got 1031 lines. About half of the 1031 lines are mapped to wrong chromosomes. Could you please tell me if 33mers is too short to run blat? What is the minimum sequence length for blat? Thanks.

Yueming Ding
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609