[Genome] The problem in the results of BLAT linux v34

[Galt Barber]

Looks like you are using the hard-masked version of the chromosomes.
I recommend using the soft-masked versions.  There are many
repeats around the exons in question and that could affect
the alignments.

For the question about the score that hgBlat generates,
please see the blat FAQ:

http://hgwdev.cse.ucsc.edu/FAQ/FAQblat#blat4

Also, note that if you are doing batch queries
it may be easier to just use stand-alone commandline
"blat" instead of gfServer/gfClient.

If memory is tight you can do one chrom at a time
and then combine/filter psl results with pslReps
and other tools like that.

-Galt


On Tue, 27 Feb 2007, wang xiaosong wrote:

> Dear All,
>
> I'm Xiaosong Wang From Dr. Arul Chinnaiyan's lab at the University of
> Michigan. We encountered a problem in the output of the BLAT linux version
> 34. The linux version of BLAT usually overlook one exon at either end of
> the input sequence. For example, the chromosome matched regions of ERG and
> TMPRSS2 sequences are 0-1128 and 55-1725 as mapped by the BLAT linux v34,
> while the matched regions were changed to 1-1514 and 1-1725 with the
> web-based BLAT(See attached file for BLAT results, and test.txt for the
> sequence). The linux version BLAT lost the last exon of ERG (1128-1514) and
> the First exon of TMPRSS2 (0-55).  The command line we use is as following:
> -----------------------------------------------
> gfServer start path-t1 7855 *.nib -minMatch=1
> gfClient path-t1 7855 /data/chromnibmasked /data/test.fa /data/test.out
> -t=dna -q=rna -minScore=0 -minIdentity=0
> -----------------------------------------------
> In addition, we find that the score in the web-based blat results was not
> provided in the linux version results. Therefore, we wonder whether anyone
> knows the algorism behind this score.
>
> Thank you very much indeed.
>
> Xiaosong
>
>
> Xiaosong Wang
> Department of Pathology, University of Michigan Medical School
> 1150 W.Medical Center Dr. Rm3232, Med Sci I, Ann Arbor, MI 48109
> Phone: 734-763-1224
>
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