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Downloading all CSHL long RNA seq data from UCSC FTP server

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  • Downloading all CSHL long RNA seq data from UCSC FTP server

    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
    Last edited by superfly; 01-03-2013, 05:18 AM.

  • #2
    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?

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    • #3
      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/

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