Number of reads in FASTQ file

[Parharn]

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

Thanks,
Parham

[Wallysb01]

wc -l file.fastq will give you the number of lines, then you can divide that by four.

Or you can just run fastqc.

[JackieBadger]

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

[Parharn]

Thanks guys.