Nucleotide statistics for fasta sequences
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6.7 years ago
l.souza ▴ 80

I have a FASTA file with 200 sequences, and I would like to know the average of nucleotides. How can I get it?

sequences • 4.7k views
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I edited the title to be consistent with the question.

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6.7 years ago
awk '/^>/ {N++;next;} {B+=length($0);} END {printf("%f\n",B/N);}' input.fasta
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Thank you, Pierre Lindenbaum!

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6.7 years ago
seqkit stats input.fasta

Look at avg.len field and link to seqkit: http://bioinf.shenwei.me/seqkit/download/

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