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Old 07-12-2011, 03:52 PM   #7
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Location: USA

Join Date: Apr 2010
Posts: 102

Sorry I missed "^" with @. It should be grep "^@" -c <filename>. However I agree with kmcarr that '@' is a character that may appear in fastq quality lines as well (sometimes at the start of the line) and so even that may not work. So the best way to do it is in two lines: wc -l <filename> followed by expr <no.of.lines> / 4
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