UCSC Golden Path - which directory to use?

Question

[sfcarroll]

On the UCSC ftp download site, there seem to be multiple options for downloading assembly data.

For example, the hg19 assembly can be downloaded from here:

ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/bigZips/

Or here:

ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/

Judging by the file sizes and dates, these seem to be the same files, possibly even a symlinked directory.

Is the correct place to start for assemblies the ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes directory?

Answer 1

[Devon Ryan]

Homo_sapiens is in fact a symlink to ../hg19. If you just want the most recent release then use the currentGenomes directory. If you want to get hg19 in a few months then that won't work, but the second link likely will (hg19 is actually the previous release, so I'm surprised the first link doesn't go to hg38).