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Old 05-18-2010, 09:24 AM   #1
Magnus
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Location: Uppsala, Sweden

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Default SOLiD and Velvet 0.7.63

Hi

I'm trying to run Velvet on SOLiD data. Have done as follows:

Compiled Velvet with color-space support, and increased hash size support.
Code:
make 'MAXKMERLENGTH = 50' & color
Creates a data set as follow:
Code:
velveth_de Sample20_hash41 41 -short Sample20.csfasta
And then run velvetg_de as follow:
Code:
velvetg_de Sample20_hash41
This gives 0 contigs in contigs.fa. Started to check other hash sizes 21, 31 and 41. All resulting in 0 contigs. I know that this data should have some contigs as ~45 % was successfully aligned with MosaikAligner.

I noticed that all sequences in file "Sample20_hash41/Sequences" has the exact same sequence "TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA". Is this normal?

Did I miss some crucial step?

Best
/Magnus
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Old 05-18-2010, 11:11 PM   #2
KevinLam
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Have you ran the preprocessor and postprocessor and denovoadp scripts from ABI?
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Old 05-20-2010, 07:23 AM   #3
Magnus
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Quote:
Originally Posted by KevinLam View Post
Have you ran the preprocessor and postprocessor and denovoadp scripts from ABI?
No, sorry, I'm new to this (Velvet with color-space). Where can I find information on how to do this?

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Magnus
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Old 05-20-2010, 10:28 PM   #4
Chipper
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http://solidsoftwaretools.com/gf/project/denovotools/
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Old 05-21-2010, 10:31 AM   #5
ondovb
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Also check out this thread.
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