[Genome] a question on local blat
Ann Zweig
ann at soe.ucsc.edu
Wed Jul 25 09:18:26 PDT 2007
Hello Jia Hui,
Can you please send me the exact command line parameters that you used
to make the call to your local copy of BLAT? No need to cc the entire
list. I will try to reproduce your results and see if I can determine
what's going on.
In the mean time, if you are interested in replicating the on-line BLAT
results, you can read this FAQ: http://genome.ucsc.edu/FAQ/FAQblat#blat5
Regards,
----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
JIA Hui wrote:
>
>
> Dear Sir,
>
>
>
> When I did local blat, I found a problem that one query got 5 100% same
> hits.
>
> The query sequence is :
>
>> AK054921__NM_004065__1
>
> ccagataatcctgagcttccagaaaatccacatcttccagacaatccatgtcttccggac
>
> aatccatgtcttccaagaagctccaagtcttccagtaaatcaagtcttccagcaaatcca
>
> gtcttccagcaattactggtcttccaccaaatccagatcttccaggaaaatccacgtctt
>
> ccaggaaatccatgtcttccaataatttcaaggtcttccatcaaatacagatcttccagc
>
> taatccatgtcttccagaaaaatctgtgtcttccaccaaatccaagtcttccagtaaatc
>
> tagttcttccagaaaaatctagatcttccagtcaatcagtgtcttccagaaagaaatcca
>
> ggtcttccagtcaatcagtgtcttccagaaagaaatccaggtcttccagtcagtcagtgt
>
> cttccagaaaaatctacgtcttccaccaaatccaggtcttccagtcaatccacatcttcc
>
> ggaaaaaatccaggtcttccagccaatatatgtcttcctgaagatccacgtcttccagaa
>
> aatccatgtcttccagaaaatccatgtcttccagtaacctcccagtcttccagaaaatcc
>
> acgtcttcccaacaatccaagtcttccggataatttgggtcttcctgaaaatctacgtct
>
> tccaaaaaagccatgtcttccagaaaatccacatcttccaatggcctccaggtcttccag
>
> actatccatgtcttccagaaaatccttgtcttcccttaaatctatagcttccaaaaaatc
>
> cgggtcttccaggaaatccgtgtcttccagcaagtccacgtcttccaacaaagccatgtc
>
> ttccagactatccatgtcttccagaaaatccttgtcttccctcaaatccatagcttccga
>
> aaaatccaggtcttccaggaaatccgtgtcttccagcaaatccacgtcttccaacaaagc
>
> catgtcttccatcaaattaatgtcttccagcctacttgtgtcttccaacaaaggtacgtc
>
> ttccaacaaaggtacgtcttccaacaaaggtatgtcttccaacaaaggtacgtcttccag
>
> aaaatccacgtct
>
>
>
> the database is hg18.2bit. all the parameters I set are default. The
> following is the local blat result.
>
> You can see that the first five lines are same.
>
>
>
> 1093 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 0 1093 chrX
> 154913754 139693090 139694183 1
> 1093, 0, 139693090,
>
> 1093 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 0 1093 chrX
> 154913754 139693090 139694183 1
> 1093, 0, 139693090,
>
> 1093 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 0 1093 chrX
> 154913754 139693090 139694183 1
> 1093, 0, 139693090,
>
> 1093 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 0 1093 chrX
> 154913754 139693090 139694183 1
> 1093, 0, 139693090,
>
> 1093 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 0 1093 chrX
> 154913754 139693090 139694183 1
> 1093, 0, 139693090,
>
> 978 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 115 1093 chrX
> 154913754 139693205 139694183 1
> 978, 115, 139693205,
>
> 972 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 121 1093 chrX
> 154913754 139693211 139694183 1
> 972, 121, 139693211,
>
> 923 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 170 1093 chrX
> 154913754 139693260 139694183 1
> 923, 170, 139693260,
>
> 901 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 192 1093 chrX
> 154913754 139693282 139694183 1
> 901, 192, 139693282,
>
> 899 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 194 1093 chrX
> 154913754 139693284 139694183 1
> 899, 194, 139693284,
>
> 895 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 198 1093 chrX
> 154913754 139693288 139694183 1
> 895, 198, 139693288,
>
> 885 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 203 1088 chrX
> 154913754 139693293 139694178 1
> 885, 203, 139693293,
>
> 574 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 280 854 chrX
> 154913754 139693370 139693944 1
> 574, 280, 139693370,
>
> 555 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 291 846 chrX
> 154913754 139693381 139693936 1
> 555, 291, 139693381,
>
> 547 0 0 0 1
> 126 0 0 +
> AK054921__NM_004065__1 1093 298 971 chrX
> 154913754 139693388 139693935 2
> 516,31, 298,940, 139693388,139693904,
>
> 511 0 0 0 0
> 0 0 0 +
> AK054921__NM_004065__1 1093 302 813 chrX
> 154913754 139693392 139693903 1
> 511, 302, 139693392,
>
> and the result of local blat is different from that webbased from ucsc
> (default parameter). The following is the result from ucsc
>
>
> BLAT Search Results
>
> ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO
> STRAND START END SPAN
> ------------------------------------------------------------------------
> ---------------------------
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693091-1396941
> 83&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693090&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693090&r=139694183&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 1093 1 1093 1093 100.0%
> X + 139693091 139694183 1093
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693430-1396940
> 61&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693429&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693429&r=139694061&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 286 49 845 1093 85.8%
> X + 139693430 139694061 632
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693123-1396936
> 45&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693122&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693122&r=139693645&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 233 531 971 1093 84.0%
> X + 139693123 139693645 523
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693767-1396942
> 22&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693766&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693766&r=139694222&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 202 16 609 1093 77.2%
> X + 139693767 139694222 456
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693656-1396942
> 13&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693655&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693655&r=139694213&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 196 286 745 1093 85.9%
> X + 139693656 139694213 558
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693031-1396935
> 53&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693030&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693030&r=139693553&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 164 657 1043 1093 80.2%
> X + 139693031 139693553 523
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693106-1396936
> 64&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693105&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693105&r=139693664&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 152 532 918 1093 87.1%
> X + 139693106 139693664 559
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693728-1396944
> 32&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693727&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693727&r=139694432&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 148 212 573 1093 86.0%
> X + 139693728 139694432 705
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693511-1396942
> 97&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693510&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693510&r=139694297&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 112 16 503 1093 92.4%
> X + 139693511 139694297 787
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693538-1396940
> 60&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693537&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693537&r=139694060&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 112 354 627 1093 90.5%
> X + 139693538 139694060 523
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693086-1396935
> 53&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693085&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693085&r=139693553&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 110 657 1061 1093 82.8%
> X + 139693086 139693553 468
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693761-1396942
> 24&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693760&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693760&r=139694224&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 73 190 464 1093 88.3%
> X + 139693761 139694224 464
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693804-1396943
> 67&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693803&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693803&r=139694367&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 69 34 275 1093 91.6%
> X + 139693804 139694367 564
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693414-1396942
> 14&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693413&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693413&r=139694214&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 54 457 564 1093 91.1%
> X + 139693414 139694214 801
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693572-1396939
> 61&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693571&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693571&r=139693961&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 45 349 600 1093 92.4%
> X + 139693572 139693961 390
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:139693447-1396934
> 81&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/h
> gSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=139693446&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chrX&l=139693446&r=139693481&db=hg18&h
> gsid=95444233> AK054921__NM_004065__1 27 707 741 1093 88.6%
> X + 139693447 139693481 35
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr10:90896020-9089604
> 7&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/hg
> Ss_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=90896019&g=htcUserAli&i=../trash/h
> gSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6b
> d990.fa+AK054921__NM_004065__1&c=chr10&l=90896019&r=90896047&db=hg18&hgs
> id=95444233> AK054921__NM_004065__1 25 419 448 1093 82.2%
> 10 - 90896020 90896047 28
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr11:80358986-8035901
> 3&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/hg
> Ss_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=80358985&g=htcUserAli&i=../trash/h
> gSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6b
> d990.fa+AK054921__NM_004065__1&c=chr11&l=80358985&r=80359013&db=hg18&hgs
> id=95444233> AK054921__NM_004065__1 24 231 257 1093 96.3%
> 11 + 80358986 80359013 28
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr11:25661864-2566188
> 7&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/hg
> Ss_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=25661863&g=htcUserAli&i=../trash/h
> gSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6b
> d990.fa+AK054921__NM_004065__1&c=chr11&l=25661863&r=25661887&db=hg18&hgs
> id=95444233> AK054921__NM_004065__1 22 413 435 1093 100.0%
> 11 - 25661864 25661887 24
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6:81315591-81315611
> &db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/hgS
> s_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=81315590&g=htcUserAli&i=../trash/h
> gSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6b
> d990.fa+AK054921__NM_004065__1&c=chr6&l=81315590&r=81315611&db=hg18&hgsi
> d=95444233> AK054921__NM_004065__1 21 314 334 1093 100.0% 6
> - 81315591 81315611 21
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr12:100415459-100415
> 481&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/
> hgSs_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=100415458&g=htcUserAli&i=../trash/
> hgSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6
> bd990.fa+AK054921__NM_004065__1&c=chr12&l=100415458&r=100415481&db=hg18&
> hgsid=95444233> AK054921__NM_004065__1 21 803 825 1093 95.7%
> 12 - 100415459 100415481 23
> browser
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr12:84962019-8496203
> 8&db=hg18&ss=../trash/hgSs/hgSs_genome_13f2_6bd990.pslx+../trash/hgSs/hg
> Ss_genome_13f2_6bd990.fa&hgsid=95444233> details
> <http://genome.ucsc.edu/cgi-bin/hgc?o=84962018&g=htcUserAli&i=../trash/h
> gSs/hgSs_genome_13f2_6bd990.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_13f2_6b
> d990.fa+AK054921__NM_004065__1&c=chr12&l=84962018&r=84962038&db=hg18&hgs
> id=95444233> AK054921__NM_004065__1 20 342 361 1093 100.0%
> 12 - 84962019 84962038 20
>
> could you tell me why this happened. Many thanks in advance
>
> Best Regards,
>
> Jia Hui
>
> Information & Mathematical Sciences
>
> Genome Institute of Singapore
>
> 60 Biopolis Street, #02-01, Singapore 138672
>
> DID: 6478 8652
>
>
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