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Old 06-19-2011, 09:30 AM   #1
MikeyG
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Location: Colorado

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Default Velvet and Oases - choice of k value?

Hi all,
I am using Velvet and Oases to assemble a transcriptome (de novo - no genome available) from unpaired short reads. The k-mer value which yields the highest average length of the transcripts which constitute the final output from Oases is different from the k-mer value which yields the highest N50 value for the contig lengths. In that case, which k-mer value should I choose and why?

Related, the kmer value yielding the highest average length of transcripts also yields more blast results than the kmer value yielding highest N50. For annotation purposes, it would seem more blast results = better choice. Is there a potential complication in using the kmer value yielding highest average length over the kmer value yielding highest N50?

Lastly, if I want to combine assemblies for different k-mer values using Vmatch software, do I use the contigs output by Velvet or the transcripts output by Oases? Which would be more appropriate?

Are there publicly available software to assemble transcripts output by Oases corresponding to different k-mer values?

As always, thanks so much for all of your help!
Cheers,
Mikey
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Old 08-22-2011, 06:57 AM   #2
scalabrin
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Location: Udine, Italy

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Quote:
Originally Posted by MikeyG View Post
Hi all,
I am using Velvet and Oases to assemble a transcriptome (de novo - no genome available) from unpaired short reads. The k-mer value which yields the highest average length of the transcripts which constitute the final output from Oases is different from the k-mer value which yields the highest N50 value for the contig lengths. In that case, which k-mer value should I choose and why?

Related, the kmer value yielding the highest average length of transcripts also yields more blast results than the kmer value yielding highest N50. For annotation purposes, it would seem more blast results = better choice. Is there a potential complication in using the kmer value yielding highest average length over the kmer value yielding highest N50?

Lastly, if I want to combine assemblies for different k-mer values using Vmatch software, do I use the contigs output by Velvet or the transcripts output by Oases? Which would be more appropriate?

Are there publicly available software to assemble transcripts output by Oases corresponding to different k-mer values?

As always, thanks so much for all of your help!
Cheers,
Mikey
We are working on a tool, GAM http://services.appliedgenomics.org/software/gam/, that does that.
At the moment it is Sanger based but we are close to a NGS release. In the first version it will merge different assemblies (different tools or same tool with different parameters, e.g. kmers) for the same set of reads.

Best,
Simone
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Old 08-23-2011, 05:34 AM   #3
Zigster
(Jeremy Leipzig)
 
Location: Philadelphia, PA

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Quote:
Is there a potential complication in using the kmer value yielding highest average length over the kmer value yielding highest N50?
no, looks like you have found a metric that works for you. N50 is not the last word in assemblies.

Quote:
Lastly, if I want to combine assemblies for different k-mer values using Vmatch software, do I use the contigs output by Velvet or the transcripts output by Oases? Which would be more appropriate?
This approach is fairly innocuous (it just clusters sequences with 100% one-sided overlap), you can run it on the transcripts.
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Old 12-10-2011, 06:38 PM   #4
upendra_35
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Location: USA

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Quote:
Originally Posted by MikeyG View Post
Hi all,
I am using Velvet and Oases to assemble a transcriptome (de novo - no genome available) from unpaired short reads. The k-mer value which yields the highest average length of the transcripts which constitute the final output from Oases is different from the k-mer value which yields the highest N50 value for the contig lengths. In that case, which k-mer value should I choose and why?

Related, the kmer value yielding the highest average length of transcripts also yields more blast results than the kmer value yielding highest N50. For annotation purposes, it would seem more blast results = better choice. Is there a potential complication in using the kmer value yielding highest average length over the kmer value yielding highest N50?

Lastly, if I want to combine assemblies for different k-mer values using Vmatch software, do I use the contigs output by Velvet or the transcripts output by Oases? Which would be more appropriate?

Are there publicly available software to assemble transcripts output by Oases corresponding to different k-mer values?

As always, thanks so much for all of your help!
Cheers,
Mikey
Currently i may not help you with your first few questions as i have just started velvet/oases. But your query regarding the publicly available software to assemble transcripts output with different k-mers you can use CAP3. It is very user friendly one-liner command tool.
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Old 12-11-2011, 12:39 PM   #5
bioBob
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Oases comes with its own method for doing this, why not use this?
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Old 05-08-2014, 09:48 PM   #6
krunal
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Location: india

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vel vet work properly with my system but after oases instalation i am not be able to run that every time i got error that is:
molbio@molbio-System-Product-Name[oases_0.2.8] oases --help [10:59AM]
zsh: permission denied: oases
molbio@molbio-System-Product-Name[oases_0.2.8] oases [11:18AM]
zsh: permission denied: oases
molbio@molbio-System-Product-Name[oases_0.2.8]
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