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Old 04-18-2011, 12:45 PM   #5
Location: USA

Join Date: Apr 2010
Posts: 76
Default Solved!

We finally realized that the FTP of the sequencing center that gave us the files was set to ASCII mode when it should have been set to binary mode. Fixing that fixed this problem.

If you're using Wget, by default it will use binary mode according to the manual.

Thanks @genelab for the helpful suggestions before...
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