I have a lot of coordinates for an assembly and want to extract the corresponding sequences. What is the best way to proceed?
Response: There are two ways to extract genomic sequence in batch from an assembly: A. Download the appropriate fasta files from our ftp server and extract sequence data using your own tools or the tools from our source tree. This is the recommended method when you have very large sequence datasets or will be extracting data frequently. Sequence data for most assemblies is located in the assembly’s “chromosomes” subdirectory on the downloads server. For example, the sequence for human assembly hg17 can be found in ftp://hgdownload.cse.ucsc.edu/goldenPath/hg17/chromosomes/. You’ll find instructions for obtaining our source programs and utilities here. Some programs that you may find useful are nibFrag and twoBitToFa, as well as other fa* programs. To obtain usage information about most programs, execute it without arguments. B. Use the Table browser to extract sequence. This is a convenient way to obtain small amounts of sequence. • Create a custom track of the genomic coordinates in BE
