Hello, The alignment to chr7 is fragmented in your result.
Here is the FAQ for BLAT: http://genome.ucsc.edu/FAQ/FAQblat If you are instead trying to replicate the RefSeq Genes track results, add the option -fine to the command string to pick up (more) terminal exons. This makes the search more sensitive, but the cost is in time/processing resource. At UCSC, we use this option for high quality transcripts. We do not offer -fine as a web BLAT option. Please note that there will always be corner cases where results differ due to hardware, software, OS version, and other various reasons related to your compute environment and ours. The version of BLAT between the Browser tracks, web BLAT, and download BLAT package are all slightly different. None of this should cause significant differences. Try the options above and if you still continue to see large, significant differences first eliminate potential problems with the install on your system, then send more detail (example of difference, percent of total with difference) and we can try to help. Thank you, Jennifer Jackson ----- Original Message ----- From: zhidong zhu <[email protected]> To: [email protected] Sent: Tue, 14 Jul 2009 20:38:36 -0700 (PDT) Subject: [Genome] How to obtain the identical result like your web supported Dear UCSC Team: I build your blat system locally. When I run gfClient, I obtained a different result from what I obtained from your web. How can I obtain the identical result like your web supported. The different points: 1. the first match result: my local result chromosome is "chr3", while your web result is "chr7" 2. not perfect match occurred in my local result, while your web result only shows 16 block perfectly match the chr7. My command: ./gfClient 10.4.0.58 17779 ./ test_seq test_blast8 -t=rna -q=dna -out=blast8 The content of test_blast8 is below: gi|27881504|ref|NM_005692.3| gi|16|ref|chr3| 93.44 1935 118 3 50 1982 88448934 88450861 0.0e+00 3384.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 271 0 0 1980 2250 150536126 150535856 2.5e-152 535.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 213 0 0 266 478 150553007 150552795 1.8e-116 416.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 204 0 0 1642 1845 150543101 150542898 3.4e-112 402.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 196 0 0 70 265 150554519 150554324 4.3e-107 385.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 183 0 0 479 661 150552133 150551951 1.3e-99 360.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 172 0 0 662 833 150551868 150551697 1.7e-93 340.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 134 0 0 1846 1979 150542210 150542077 1.5e-70 263.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 129 0 0 1513 1641 150543751 150543623 5.7e-67 252.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 120 0 0 1129 1248 150546892 150546773 2.6e-62 236.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 111 0 0 1339 1449 150546210 150546100 1.6e-56 217.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 103 0 0 930 1032 150549699 150549597 2.0e-51 200.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 96 0 0 834 929 150550635 150550540 7.0e-48 188.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 96 0 0 1033 1128 150547178 150547083 1.0e-47 188.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 85.12 121 18 0 1843 1963 71206996 71207116 1.3e-45 181.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 86.21 116 16 0 1727 1842 71206141 71206256 1.8e-45 180.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 90 0 0 1249 1338 150546669 150546580 6.7e-44 175.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 69 0 0 1 69 150555250 150555182 1.5e-32 137.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 63 0 0 1450 1512 150544048 150543986 2.7e-28 123.0 gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 93.75 32 2 0 1690 1721 71206102 71206133 8.0e-09 58.0 zhidong zhu national biochip engineering center at shanghai. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
