Scaffolding problem with Velvet

[Melissa]

Hi,

Does anyone has problem with scaffolding using velvet? The contigs I generated are small and do not contain Ns.

I'm sure I follow the manual:
-First I merge the paired end reads using shufflesequences.pl
-./velveth for shortPaired
-./velvetg for paired-ends by giving insert size and expected coverage

What went wrong?

[avt]

try some large exp_cov, and how did you run Velveth
Can you tell me how big is your data? I often fail to run it on my (big) file..!

[Melissa]

My data is around1.3Gb.