Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • Kennels
    Senior Member
    • Feb 2011
    • 149

    #1

    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.

Latest Articles

Collapse

  • SEQadmin2
    Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
    by SEQadmin2



    Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

    Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
    ...
    10-14-2026, 09:55 AM
  • SEQadmin2
    New Genomics Technologies Take Aim at Long-Standing Limits
    by SEQadmin2


    Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

    We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing
    ...
    09-28-2026, 10:25 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 10-15-2026, 10:52 AM
0 responses
31 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-14-2026, 05:39 AM
0 responses
38 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-13-2026, 09:56 AM
0 responses
31 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-09-2026, 11:14 AM
0 responses
29 views
0 reactions
Last Post SEQadmin2  
Working...