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  • 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.

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