On 15/07/12 00:08, Hiram Clawson wrote: > Good Afternoon Tony: > > Your 20 GiB database is inefficient and too large to function. > Break up your database into about 10 pieces, 2 GiB each and run > your queries against those 10 pieces.
Hi, Hiram. BLAT works very well on my 20GiB DB - when it doesn't segfault! I'm loading it from a file of files, in 2bit format, and it is *stunningly* faster than BLAST of the same DB. I created one 2bit file from each record in a FASTA format file we downloaded from Ensemble: Homo_sapiens.GRCh37.67.dna.toplevel.fa What advice would you give me to BLAT the human genome efficiently? Thanks, Tony. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
