[Genome] blat -minIdentity

[Brooke Rhead]

Hello Yueming,

It could be that there are simply are no more hits for any these 25mers 
(although that seems somewhat unlikely, since it sounds like you have 
tried this with several 25mers).  Or it could be that none of the hits 
score above 20, and the -minScore=20 setting is keeping any more hits 
from coming up.

One of our engineers has also mentioned that BLAT's sensitivity 
requirements are high enough that a low minIdentity will often not pick 
up more hits.  He suggested that you try the -fine setting.

If you would like to send a specific example where hits are not being 
found, we can try to determine what is happening.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

We invite you to give us your feedback on the UCSC Genome Browser
through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177




Yueming Ding wrote:
> Generator Microsoft Word 11 (filtered medium) Hi I have a problem with - minIdentity in using blat. I tried the following command line:
> blat mouse_genome.fa seqs.fa seqs.psl - minScore=20 - noHead - tileSize=8 - stepSize=5 - noTrimA
>
> The seqs.fa are 25mers.
>
> If I add - minIdentity=95, I' ll get less hits, which makes sense. But if I add - minIdentity=85, or - minIdentity=80, or - minIdentity=70, I still get the same number of hits as I used the default (- minIdentity=90). Could you please tell me why I couldn' t get more hits if I used the smaller number of - minIdentity than the default? Thanks.
>
> Yueming Ding
> The Jackson Laboratory
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