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
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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