Dear UCSC Genome Browser team, We have problems to recover your online blat search results with our local blat searches. Our problem is that we get a lot more hits than the online search reports but we can not figure out why they are not reported.
We are using the stand alone blat version with the same parameters as suggested on the FAQ page and I compute the score like you do in your script (psl.c). We are blatting DNA and use the same genome version. blat -stepSize=5 -repMatch=1024 -minScore=0 -minIdentity=0 canFam2.2bit in.fa temp.psl (pslWithScores.psl has the score and a percent identity in its first two columns and in temp.psl you will find the output file from the local blat search). When we blat the sequence attached (in.fa) we get the best score 597, while the web-tool's best hit has the score 106. As you can see, we also get this hit (so the computation of the score is correct), but we also get a lot more (and not few better ones). Is it something we need to change about the parameters or do we need to filter the results afterwards? Here is an example: 138 22 0 0 5 349 5 228 + Emx2os_Human 7282 3898 4407 chr24 50763139 31027810 31028198 7 66,27,8,10,7,8,34, 3898,3977,4014,4038,4048,4358,4373, 31027810,31027890,31027925,31028034,31028107,31028156,31028164, This is your best match (according to the online tool) as is in the psl output file, which scores 106. 774 121 0 0 27 3588 29 60189 - Emx2os_Human 7282 69 4552 chr28 44191819 30945073 31006157 33 8,4,17,8,32,29,51,12,22,95,17,15,31,8,38,6,6,36,38,6,16,39,10,7,24,21,22,67,10,22,144,28,6, 2730,2744,2749,2766,2780,2889,3578,3683,3703,3730,3950,3977,3999,4060,4068,4107,4113,4537,4729,4774,4781,6119,6164,6232,6246,6352,6373,6788,6943,6966,6992,7179,7207, 30945073,30945094,30945098,30945116,30945129,30945237,30945598,30945689,30945719,30945742,30945974,30946002,30946023,30946079,30946098,30946136,30946143,30946252,30946463,30946509,30946520,30946607,30946651,30946708,30946719,30946823,30946845,31005736,31005884,31005908,31005930,31006116,31006151, This is the highest scoring hit we got. The score is 597, but between this one and 106 there are many better scores. Why do you not report this hits? Kind regards, ilinca tudose
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