counting the number of reads in FASTQ files

Question

[Ric]

Hi, I would like to get the read coverage and I found here C = LN / G whereas:

• C stands for coverage
• G is the haploid genome length
• L is the read length
• N is the number of reads

How is it possible to count the number of reads in FASTQ files?

Thank you in advance

[Mark]

How to count fastq reads

on a different note, I know you didn't ask but there's software to count read depth and coverage.

[h.mon]

The same question has been asked a number of times, e.g.

How to count fastq reads

Sequence Number Count In Fastq.Gz File

Answer 1

[swbarnes2]

wc -l mysample.fastq

or

zcat mysample.fastq.gz | wc -l

Then divide by 4.

But I strongly doubt every read in the fastq is going to align to your genome. So I don't see how this number helps.