Question about preventing N's from Oases assembly

Kennels

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Question about preventing N's from Oases assembly

07-09-2013, 07:00 PM

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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