Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • syintel87
    Member
    • Dec 2012
    • 81

    #1

    [SOAPdenovo] coverage cut off

    Hello.
    While running SOAPdenovo assembler, I have a question about parameter setting.

    What I want to do are set different coverage cut offs and compare the results.
    So the commands that I used are
    Code:
    srun SOAPdenovo-127mer all -s chitwood1.config -K 127 -o 127mer10c [B]-c 10[/B] -V >127mer10c.out 2>&1 &
    srun SOAPdenovo-127mer all -s chitwood1.config -K 127 -o 127mer15c [B]-c 15[/B] -V >127mer15c.out 2>&1 &
    srun SOAPdenovo-127mer all -s chitwood1.config -K 127 -o 127merDf [B]-c 4.6[/B] -V >127merDf.out 2>&1 &
    However, all three running gave me exactly the same results.
    (In case of Velvet and ABySS, they gave the different results.)

    My questions are
    - Is the option "-c" not for coverage cut off?
    - If not, what option do I have to use to set a particular coverage cut off?

    Thanks in advance.

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
23 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-14-2026, 05:39 AM
0 responses
29 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-13-2026, 09:56 AM
0 responses
25 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-09-2026, 11:14 AM
0 responses
28 views
0 reactions
Last Post SEQadmin2  
Working...