Question: How to check size of genome?
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arianc • 0 wrote:
Hey! It is possible to check the size of genome (number of bp) in bam (or sam or fastq) file?
Thanks in advance.
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modified 12 days ago
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Alex Reynolds ♦ 31k
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12 days ago by
arianc • 0
You are not checking the size of the genome if you are simply looking at your raw or aligned data. You are just counting the number of bases sequenced.
If you want to estimate size of the genome then you need to do something like this.
I want to know how to check number of base pairs in bam file
You could simply run
reformat.sh -Xmx10g in=your.bam
from BBMap suite. It will produce output that will contain this information.mappedonly=t
etc should modify the output. Test it out.That's not the same as the size of the genome though. What exactly do you want?