Hello I have been using the standalone Blat extensively over the last few months using the following command :
blat -stepSize=5 -minScore=0 -minIdentity=0 database.2bit query.fa output.psl which replicates the web-based version of the same as specified on the website (http://genome.ucsc.edu/FAQ/FAQblat). However, I have run into an issue where there is a significant difference in the results. For example, On using the web-based Blat based on the following : Genome : Mouse Assembly : July 2007 Query Type : DNA Sequence : ATTTGTGTGTGTGTGTGTGTTTTTTTTTTTGTTGTTGTTGTTGTTGTTGTTTTGAGACAGGGTTT The result obtained is QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- YourSeq 65 1 65 65 100.0% 16 + 62887839 62887903 65 However, on using the standalone blast, the same sequence yields no results. Kindly, let me know where the problem lies? Thank you Amol Carl Shetty Department of Human Genetics Emory University Atlanta, Georgia _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
