Downloading all CSHL long RNA seq data from UCSC FTP server

[superfly]

Hello there,

I'm trying to download all the bam & bam.bai files of ENCODE's CSHL long RNA seq data for a particular genomic locus using Perl from the UCSC FTP server.

I tried downloading the whole genome RNA seq bam file for one cell line initially, but its too painstaking.. If anyone could please suggest a way or if anybody already has got a Perl script for this, could you please share? I'd be umpty grateful!

Best,
Vaish

[qzyfy1]

I met another problem. When I try to download each ENCODE data file the webpage would return a error. Could anyone download such CSHL long RNA seq data as normal?

[kuod]

Hopefully you've solved your problems but I've found lftp to be the best command line program to effectively 'mirror' one directory to another.

More info here:

http://www.cyberciti.biz/faq/lftp-mirror-example/