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Hi,
How can I just find out how many reads are there in a fastq file?
Thanks,
Parham
How can I just find out how many reads are there in a fastq file?
Thanks,
Parham
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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. -
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.fastqLast edited by JackieBadger; 02-17-2014, 11:34 AM.Comment
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Thanks guys.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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