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Old 07-12-2011, 12:58 PM   #5
kmcarr
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Location: USA, Midwest

Join Date: May 2008
Posts: 1,178
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Quote:
Originally Posted by upendra_35 View Post
its not -1 it is -l and the command wc -l counts the number of lines in the file. The easiest way to find out the number of reads in a fastq file with one command is grep "@" -c <filename>. Hope this helps
This will not work! The '@' character may appear in fastq quality lines as well as the seq-id line. See this thread for a discussion on the problems of using grep to count reads in fastq files.
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