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Old 11-07-2016, 07:51 PM   #1
yipukangda
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Location: beijing

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Question fastq.gz size for human WGS coverage calculation

I have got 3 pair fastq.gz file of human WGS, the size are 3.9 + 4.2, 1.7 + 1.8, 1.5 + 1.6 respectively, how to calculate coverage of these results.
sequence plantform: illumina x ten
seq model: pair-end 150
thx

Last edited by yipukangda; 11-07-2016 at 09:22 PM.
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Old 11-08-2016, 10:46 AM   #2
Brian Bushnell
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If you want average coverage, assuming the data is all human:

Code:
avg_coverage=(#reads)*150/3000000000
To count the reads, you can use Reformat from the BBMap package:

Code:
cat *.fastq.gz | reformat.sh in=stdin.fq
You can get more accurate numbers by mapping the reads after adapter-trimming, since some of the data is probably not human.
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Old 11-08-2016, 06:26 PM   #3
yipukangda
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Quote:
Originally Posted by Brian Bushnell View Post
If you want average coverage, assuming the data is all human:

Code:
avg_coverage=(#reads)*150/3000000000
To count the reads, you can use Reformat from the BBMap package:

Code:
cat *.fastq.gz | reformat.sh in=stdin.fq
You can get more accurate numbers by mapping the reads after adapter-trimming, since some of the data is probably not human.
thanks, I estimated like this: file_size x 1/2 x compression fold / genome size
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