Hi Lise, The command line BLAT doesn't have the same default parameters as the web version of BLAT has, which is probably why you're seeing different results with the two methods. If you want to replicate the web BLAT results, follow these instructions:
http://genome.ucsc.edu/FAQ/FAQblat.html#blat5 I hope this is helpful. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group lise andrieux wrote, On 7/15/2011 3:59 AM: > Good morning, > > I habe been using BLAT V34 in local recently, to do dna against dna > alignement (option t=dna and q=dna) > > When I compare the results with the one obtained on the UCSC Blat page for > the same sequence, only the best hit is the same, while all the others hits > are different between local and website results. > > Please find the attached files with the dna sequence used for the Blat, the > results from the website, and the results from local blat. > > Since the sequence is on chromosome 11, the database I use for blat is only > this chromosome 11 and the file Homo_sapiens.GRCh37.62.dna.chromosome.11.fa > was obtained from Ensembl. I filtered the website blat results so that only > chromosome 11 lines appear. > > I would appreciate your help. > > Thanks and best regards, > > Lise > > Lise Andrieux, PhD > Computational Genomics > Life Sciences DPT > Barcelona Supercomputing Center > Barcelona, Catalunya, > > Spain > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
