Fasta length does not match Ensembl info
I am calculating the total genome length from a fasta file using the following code
zcat genome.fa.gz | grep -v ">" | wc | awk '{print $3-$1}'
For Yeast, I get 12,157,105, and the Ensembl info indicates exactly 12,157,105. So, that adds up.
For Human, I get 56,917,651,860, but the Ensembl info indicates 3,609,003,417.
Anyone know why? I must be missing something.
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Nicolas Rosewick
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firestar
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firestar
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here you are counting the number of lines.
You should try wc -m as mentionned in wc man page :
-m
displays a character count. You cannot specify this option with -c.
Thus :
zcat genome.fa.gz | grep -v ">" | wc -m
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edit : to count only character and not newlines :
zcat genome.fa.gz | grep -v ">" | tr -d '\n' | wc -m
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I edit my answer accordingly. You have to use tr -d '\n' to remove newlines
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From the ftp://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/dna/README:
Ah right! Ensembl count for human is based on the primary assembly. And some organisms don't have primary assemblies, just the top-level.