[Genome] optimal settings for aligning medium length oligos

[Rachel Harte]

Mark,

For aligning 50mers and 65mers, you could try reducing the tileSize and
the stepSize from the default values. However, the default values for the
web-based Blat should easily find sequence matches of 95% identity and of
lenght 40 bp or more. See this FAQ for replicating the web Blat parameters
in the command-line version:
http://genome.ucsc.edu/FAQ/FAQblat#blat5

I think that the main difference, for your purposes, is that web Blat uses
stepSize=5 as its default value.

I will also forward your e-mail to some of our engineers who may be able
to recommend more specific values to try.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Fri, 30 Mar 2007, Mark Cowley wrote:

> Hello, and thanks for providing such a fantastic resource.
>
> I am using stand alone BLAT, and aligning 50mers and 65mers to the mouse
> and human genomes.
>
> Can you please tell me the optimal settings for aligning:
> 65mers to the genome?
> 50mers to the genome?
>
> thank you
>
> Mark
>
> Mark Cowley
> PhD candidate
>
> Systems Biology Laboratory 2 (room 263)
> School of Biotechnology and Biomolecular Sciences
> University of New South Wales
> NSW, 2052, Australia
>
> email:   mark.cowley at student.unsw.edu.au
> web:     http://www.babs.unsw.edu.au/
>
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