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Old 01-23-2011, 02:08 AM   #2
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

You don't mention the specific sample you're interested in so it's difficult to give an exact answer. If the entry was deposited in base space then there won't be an option to download colorspace (since that wouldn't make any sense anyway).

If you have a .sra file instead of a direct fastq file then you can use the --dumpcs option to fastq-dump to get colorspace fastq files from the sra file.
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