I am looking for a possibility to download the complete nt DB in 2bit format. I need it to run a BLAT search against my unmapped reads from a RNA-Seq experiment. I have a lot of unmapped reads and one way to try and identify the source of these high amount of reads was to try and run a BLAT search against the complete nt. BUT BLAT takes only the 2bit format as an input. I know I can convert the fastA into 2bit, but I was wondering if there a better way than to split the fastA file into subsets (the faToTwoBit script from UCSC can't handle files bigger than 4GB).
thanks in advance