Hi Vinay, For the databases, use .2bit. For your query data, using .fa is fine.
Here is a link to the Blat parameter sets/commands we use for various tasks: http://genome.ucsc.edu/FAQ/FAQblat#blat5 Happy to help, Jennifer Jackson UCSC Genome Bioinformatics Group Mittal, Vinay K wrote: > Hi, > This might be a repeated question for you but it would be great if you can > help me here. > Which database format would you prefer for standalone BLAT? (.fa, .2bit or > .nib format) > > Thanks.. > > > Sincerely, > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
