Hi, "query" is the sequence file that you want to align. In your case it would be "sva.fa"
"database" is the sequence file that you want to align against, often some reference genome? You can get reference genomes in fasta format from: http://hgdownload.cse.ucsc.edu/downloads.html For example, the hg19 human database is here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz Which you can get with the command "wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz"; If you go here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ It has a description of the chromFa.tar.gz and some useful information. You will have to extract the .tar.gz file, and then probably concatenate them into one file, which you can do with something like: cat *.fa > hg19_genome.fa So, finally, your command to BLAT would be something like blat hg19_genome.fa sva.fa sva.psl Here is some more info about BLAT: http://genome.ucsc.edu/FAQ/FAQblat.html (look at section "Replicating web-based Blat parameters in command-line version <http://genome.ucsc.edu/FAQ/FAQblat.html#blat5>") http://genome.ucsc.edu/goldenPath/help/blatSpec.html (search the page for "blat settings for common usage scenarios") ~Lucas Lita Mallett wrote: > I have a basic question, but It is preventing me from getting any work done! > > When running blat in the command line, where do I get the database and query > from? > > I want to align a file that I have named sva.fa. I am,not exactly sure what > is meant by query and database, and where I should get them from. > > Your help is greatly appreciated. > > If possible, can you give me a step by step of how to use BLAT after it is > successfully downloaded? > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
