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Old 10-06-2014, 05:31 PM   #3
Brian Bushnell
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Location: Walnut Creek, CA

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I don't see a problem with the first 8 lines, at least. And yes, repair.sh requires correctly-formatted fastq headers; it's only for fixing broken pair ordering. I'm not familiar with how STAR deals with gzipped files, but perhaps you could try decompressing it first?
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