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We recommend that you download data via rsync using the command line, especially for large files.
For example, when downloading ENCODE files to your present directory (./), you would use an expression such as:
$ rsync -a -P rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeDir/wgEncodeFile ./
To download the entire directory (note the trailing slash), you would use an expression such as:
$ rsync -a -P rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeDir/ ./
To obtain a file's location (URL) to use with rsync (rsync://hgdownload.cse.ucsc.edu/...), you can navigate in your browser to our FTP site at ftp://hgdownload.cse.ucsc.edu/, or our downloads page at http://hgdownload.cse.ucsc.edu/downloads.html, and look for your file of interest. To learn more about rsync's options, type "man rsync" on the command line.
If you are not comfortable using the command line, you can download your file via FTP in your browser at ftp://hgdownload.cse.ucsc.edu/goldenPath, or from our downloads page at http://hgdownload.cse.ucsc.edu/downloads.html.
However, downloading via your browser will be very slow or may even time out for large files (i.e., bigBed, bigWig, BAM, VCF, etc.). Also, Safari does not support FTP inside the browser. When you enter a FTP URL in Safari, you may have to select "Guest" and click submit to login before a FTP file system will open in a window on your desktop.
$ ftp hgdownload.cse.ucsc.edu Name: anonymous Password: <your email address> ftp> cd goldenPath ftp> cd <assembly name> (e.g., hg19) ftp> cd <data directory> (e.g., liftOver)
To download multiple files from the UNIX ftp command line, use the "mget" command. You may want to use the prompt command to toggle the interactive mode if you do not want to be prompted for each file that you download.
ftp> mget [filename1] [filename2] ...
Or to download all the files in the directory:
ftp> mget -a
Please note that rsync will be much easier and quicker than using FTP. Rsync is a much more efficient and convenient transport mechanism.