fastq.gz size for human WGS coverage calculation

[yipukangda]

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

[Brian Bushnell]

If you want average coverage, assuming the data is all human:

avg_coverage=(#reads)*150/3000000000

To count the reads, you can use Reformat from the BBMap package:

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.

[yipukangda]

If you want average coverage, assuming the data is all human:

avg_coverage=(#reads)*150/3000000000

To count the reads, you can use Reformat from the BBMap package:

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