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counting the number of reads in FASTQ files

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

next-gen sequencing coverage
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updated by swbarnes2 swbarnes2 • written by Ric Ric

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.

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written by Mark Mark

1 answer 

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.

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written by swbarnes2 swbarnes2

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