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Old 02-17-2014, 09:17 AM   #1
Parharn
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Default Number of reads in FASTQ file

Hi,
How can I just find out how many reads are there in a fastq file?

Thanks,
Parham
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Old 02-17-2014, 09:22 AM   #2
Wallysb01
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wc -l file.fastq will give you the number of lines, then you can divide that by four.

Or you can just run fastqc.
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Old 02-17-2014, 09:26 AM   #3
JackieBadger
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Or

grep xxx -c file.fastq

xxx being some string of characters only found in sequence identifiers

With MiSeq generated fastq an example would be

grep @M00 -c file.fastq

Last edited by JackieBadger; 02-17-2014 at 10:34 AM.
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Old 02-17-2014, 09:41 AM   #4
Parharn
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Thanks guys.
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