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Old 12-23-2009, 01:58 AM   #1
Melissa
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Location: Switzerland

Join Date: Aug 2008
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Talking 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?
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Old 01-05-2010, 10:15 AM   #2
avt
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Location: Davis, CA

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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.
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Old 01-05-2010, 07:44 PM   #3
Melissa
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My data is around1.3Gb.
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