[Genome] repMatch field in psl

[Galt Barber]

add -repeats=lower to your blat command.

-Galt


On Thu, 31 Jan 2008, Yu Zhou wrote:

> Hello UCSC developers,
>
> Thanks a lot for your previous answers!
>
> I have another question about the repMatches field in the psl format.
> >From the definition, it is the "Number of bases that match but are
> part of repeats".
>
> However, when I ran a WEB Blat or Local Blat on a test sequence whose
> first 4 nt belong to a repeat element, the repMatch number of both
> resulted psl records were 0.
>
> >twoBitToFa /gbdb/hg18/hg18.2bit:chr1:1306-1338 test.fa
> >more test.fa
> >chr1:1306-1338
> tgctCCAACAGTACTGGCGGATTATAGGGAAA
> (The first 4nt are in lowercase, meaning in a repeat element.)
>
> >blat /gbdb/hg18/hg18.2bit:chr1:1-2000 test.fa test.psl
> >more test.psl
> match   mis-    rep.    N's     Q gap   Q gap   T gap   T gap   strand
>  Q               Q       Q       Q       T               T       T
>   T       block
>         blockSizes      qStarts  tStarts
>         match   match           count   bases   count   bases
>  name            size    start   end     name            size    start
>   end     count
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------
> 32      0       0       0       0       0       0       0       +
>  chr1:1306-1338  32      0       32      chr1:1-2000     1999    1305
>   1337    1   32,      0,      1305,
>
> What is the reason about that? Is there a program to check whether a
> Blat hit is in a repeat element? If not, could you give me a
> suggestion? (comparing the hit to the repeat tables in the hg18
> database?) Thanks a lot in advance!
>
>
> PS: Thanks a lot for the kent source package, which contains many
> useful programs, nearly all the tools I need at the moment. There are
> also many ones that I haven't tried yet.
>
>
>
> --
> Best regards,
>
> Yu Zhou
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>