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Old 10-16-2011, 11:18 PM   #1
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Location: Bangalore

Join Date: Jun 2011
Posts: 7
Default n50 value for transcriptome assembly

I am doing a Denovo transcriptome assembly using oases. I would like to know about the relation between n50 value obtained from velvet assembly and the performance of oases.
Generally a high n50 value is considered to be good in case of genome assembly. But for transcriptome assembly before proceeding with oases should I consider the hash length with high n50 value or is there any other parameter that I should consider?

For example let's consider the following statistics,
Hash length 49 57
n50 790 874
Total length of contigs 17010831 12759209

Total length of transcripts from oases is 18953313 for 49 and 16638235 for 57.

If I consider 57 as a better hash length and proceed with oases I end up losing so much after transcriptome assembly.

Thanks in advance.


Last edited by Ramprasad; 10-17-2011 at 07:27 AM.
Ramprasad is offline   Reply With Quote

hash length, oases, transcript assembly, velvet

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