Total Contig Length From Velvet Output

Question

[deepthithomaskannan]

Hi all,

I want to calculate total contig length from velvet output in bp. So I used the following method:

perl -F\\_ -ane 'BEGIN{$sum=0;$orig=0;} next unless /NODE/;$len=$F[3];$orig=$len+51-1;$sum=$sum+$orig;END{print "$sum\n";}' contigs.fa

But the result I got is different from the total value from the Log file. I am not getting the Log file total value even if I did not use $orig=$len+51-1 part. I think I am missing something. Please help me.

Thanks, Deepthi

[Eric Normandeau]

Hi deepthi. If you think that the answer from Jeremy, or any other answer, was useful to you, you can use the up arrow at the left of his answer to vote for it. Also, if it helped you solve your problem, you can click on the check mark (in green) to mark this as the solution. Cheers

Answer 1

[Jeremy Leipzig]

http://code.google.com/p/standardized-velvet-assembly-report/wiki/faq

Read the FAQ - everything is explained there.

[Eric Normandeau]

I changed the link to make it impossible not to get to the FAQ :)

[deepthithomaskannan]

Thank you very much