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Old 10-07-2009, 01:12 AM   #7
edge
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Location: China

Join Date: Sep 2009
Posts: 199
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Hi BENM,

I just try the code that you give it to me.
It can't work d.
Do I miss anything or the code got problem?
After I run the code,the output result is empty d
Thanks for your help ^^
Quote:
Originally Posted by BENM View Post
N50 = length-weighted median.: The size of the smallest contig such that 50% of the length of the genome is contained in contigs of size N50 or greater.
N90 is 90%.
If you have done the assembly work, and you have got the contigs in FASTA format, it is easy to calculate the N50 & N90 contig size, for example:
Code:
perl -e 'my ($len,$total)=(0,0);my @x;while(<>){if(/^[\>\@]/){if($len>0){$total+=$len;push@x,$len;};$len=0;}else{s/\s//g;$len+=length($_);}}if ($len>0){$total+=$len;push @x,$len;}@x=sort{$b<=>$a}@x; my ($count,$half)=(0,0);for (my $j=0;$j<@x;$j++){$count+=$x[$j];if($count>=$total/2){$half=$x[j];print "N50: $x[j]\n" if ($half==0);}elsif($count>=$total*0.9){print "N90: $x[j]\n";exit;}}'  contigs.fa
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