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Old 09-10-2011, 02:10 PM   #1
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Join Date: Sep 2011
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Smile velvet: 60bp Illimuna reads. -short or -long?

Hi folks,

I have some questions about running velvet, and I will really appreciate you guys could spare some time helping me figure it out =) =)

I have 19 mio 60b Illumina single-end reads (transcriptome), duplicates removed. Should I choose -short or -long when running velveth? I read the manual and some posts but still not sure. Thanks a lot!!!

I am thinking of trying kmer from 31 to 41. Should I try longer kmers? We have a computer with 32 cores 64GB ram. Would that be enough for running velvet+oases on my data? Any suggestions are highly appreciated!!!!

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