[Genome] blat didn't work on 33mers

[Jim Kent]

Hi - you probably want to use these blat parameters:
	-stepSize=5 -minScore=0
33mers are on the short side for accurate mapping though.
Are these mouse sequences?  From the same strain as the
genome?

On Jan 8, 2007, at 9:03 AM, Yueming Ding wrote:

> 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
>
>