Scaffolding problem with Velvet

Melissa · 12-23-2009, 01:58 AM

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 · 01-05-2010, 10:15 AM

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 · 01-05-2010, 07:44 PM

My data is around1.3Gb.

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12-23-2009, 01:58 AM	#1
Melissa Senior Member Location: Switzerland Join Date: Aug 2008 Posts: 124	Scaffolding problem with Velvet 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?

01-05-2010, 10:15 AM	#2
avt Junior Member Location: Davis, CA Join Date: Dec 2009 Posts: 3	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..! Last edited by avt; 01-05-2010 at 10:18 AM.

01-05-2010, 07:44 PM	#3
Melissa Senior Member Location: Switzerland Join Date: Aug 2008 Posts: 124	My data is around1.3Gb.