[Genome] BLAT & microreads

[Galt Barber]

Hi, Ming.

See my mail in the pipermail archives to Chris on July 31st about
blat and minScore. It appears that minScore can't really be raised above
about half of the qSize.  So if you specify a minScore
higher than qSize/2, you will still get values as low as qSize/2.

I recommend using pslCDnaFilter or pslReps to post-filter
psls, these utilities have many useful options.

Comparing to BLAST is probably worthwhile.

-Galt


On Fri, 10 Aug 2007, Minghsun Liu wrote:

> Hi,
>
> I am wondering if anyone has been using BLAT for mapping sequencing reads
> (microreads) produced by Illumina/Solexa or ABI (currently between
> 26-32mers, with up to 2 mismatches)?
>
> After reading some of the previous posts regarding short reads, I have tried
> varying several parameters such as tileSize, stepSize, and minIdentity. I
> tried specifying minScore as well but it does not seem to work (i.e. I am
> still getting hits that scored below the specified minScore). It seems to
> work fairly well for my purpose  (using oneOff=1, minMatch=1, minIdentiy=92,
> default tileSize and stepSize) but I don't have any good idea about how to
> gauge the sensitivity except comparing the results with the that from using
> BLAST. Any thoughts?
>
> Cheers,
>
> - Ming
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