Question: counting the number of reads in FASTQ files
0
gravatar for Ric
19 days ago by
Ric280
Australia
Ric280 wrote:

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

ADD COMMENTlink modified 19 days ago by swbarnes27.0k • written 19 days ago by Ric280

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.

ADD REPLYlink modified 19 days ago • written 19 days ago by Amar620

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

How to count fastq reads

Sequence Number Count In Fastq.Gz File

ADD REPLYlink written 19 days ago by h.mon28k
1
gravatar for swbarnes2
19 days ago by
swbarnes27.0k
United States
swbarnes27.0k wrote:
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.

ADD COMMENTlink written 19 days ago by swbarnes27.0k
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