This page contains links to search tools for finding tracks displayed in the browser or downloadable files from the ENCODE project at UCSC during the first ENCODE production phase (Sep 2007 - Jun 2012). For bulk download, retrieval by FTP is recommended along with rsync. Using rsync, for example "rsync -a -P rsync://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeDir/wgEncodeFile ./", has the advantage of starting up where it left off after a failure, when ran again.

Search for tracks visible in the Genome Browser - Human GRCh37/hg19 assembly.
Search for downloadable files of data aligned to the Human GRCh37/hg19 assembly.

Search for tracks visible in the Genome Browser - Human NCBI36/hg18 assembly.
Search for downloadable files of data aligned to the Human NCBI36/hg18 assembly.

Search for tracks visible in the Genome Browser - Mouse NCBI37/mm9 assembly.
Search for downloadable files of data aligned to the Mouse NCBI37/mm9 assembly.