Hi, Taek-Kyun
http://genome.ucsc.edu/FAQ/FAQblat
tileSize means the number of contiguous bases
in the target database (often a genome assembly) that are
used as an index key. If it is longer it is more
specific, but also uses more ram. The default value good for
for many nucleotide alignments is 11.
stepSize means the number of bases to shift forward to read
the next tile when building the target database index.
Of course the query side is processed as tiles too,
but in that case the stepSize is always 1.
Rather than index the negative nucleotide strand,
The query is simply reverse-complemented and then
the run again on the target index.
repMatch refers to the number of hits on a tile
before the tile is marked as over-used and becomes
masked out.
-maxGap=N sets the size of maximum gap between tiles in a clump.
Usually set from 0 to 3. Default is 2. Only relevent for minMatch > 1.
-minMatch=N sets the number of tile matches. Usually set from 2 to 4
Default is 2 for nucleotide, 1 for protein.
This is a useful way to filter out noisy time-consuming hits that are of
low-value. By requiring that there be two hits along the same diagonal
for the query before further expensive processing is done, speed is
greatly increased with only a small decrease in sensitivity.
A maxGap of 0 means that the two hits have to be exactly on the same
diagonal, whereas increasing maxGap allows it to tolerate small indels
of 1 to 3 bp.
---
There are some very good specialized small-read aligners available these
days such as MAQ and Bowtie.
-Galt
> Dear administrator
>
>
>
> I am Taek-Kyun, a researcher at POSTECH in Korea. I’m so glad to meet you
> through this e-mail.
>
> I have some difficulty in implementing the BLAT program.
>
> Although I’ve seen the option of the program, I cannot understand it, the
> biggest problem is the word used in the option.
>
>
>
> I’m trying to align the database with the very short sequence (the
> sequence size : 20 bp). And I want to allow the gap option of more than 2bp.
>
> In these case, how should I install the option to get a desired result?
>
> Additionally, I want to know exactly the word’s meaning : tileSize,
> stepSize, maxGap, repMatch.
>
> There are so insufficient description in the option.
>
> Could you tell me about it? Sorry for bothering you.
>
>
>
>
>
> Take care,
>
> Thank you.
>
>
>
>
>
> From Taek-Kyun.
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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