[SOAPdenovo] coverage cut off

syintel87 · 05-01-2014, 08:48 AM

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 -c 10 -V >127mer10c.out 2>&1 &
srun SOAPdenovo-127mer all -s chitwood1.config -K 127 -o 127mer15c -c 15 -V >127mer15c.out 2>&1 &
srun SOAPdenovo-127mer all -s chitwood1.config -K 127 -o 127merDf -c 4.6 -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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05-01-2014, 08:48 AM	#1
syintel87 Member Location: Universe Join Date: Dec 2012 Posts: 81	[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 -c 10 -V >127mer10c.out 2>&1 & srun SOAPdenovo-127mer all -s chitwood1.config -K 127 -o 127mer15c -c 15 -V >127mer15c.out 2>&1 & srun SOAPdenovo-127mer all -s chitwood1.config -K 127 -o 127merDf -c 4.6 -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.