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  • Kennels
    started a topic Question about preventing N's from Oases assembly

    Question about preventing N's from Oases assembly

    Hi,

    I haven't heard back from the authors so hope someone can help me here.

    I ran a velvet/oases assembly with no scaffolding in mind.
    I am using velvet 1.2.08, and oases 0.2.08

    1. For velvetg, '-scaffold no' was set
    2. For oases, '-scaffold no' is already the default (according to the help screen), so I left as is.

    here were my commands after velveth:

    $ velvetg nlab_25 -read_trkg yes -scaffolding no
    $ oases nlab_25 -ins_length 145

    Yet, the transcripts.fa in the kmer25 assembly contains 'Ns' , which I am assuming are the 'gaps' from the scaffolding option.

    How can I make oases not scaffold?

    (I also ran oases with '-scaffolding no' option, but the transcripts.fa still produced N's in the contigs)
    Last edited by Kennels; 07-09-2013, 07:37 PM.

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