SOAPdenovo flag -F

[scami]

Hi guys I am experiencing some problem with the flag -F of SOAPdenovo. The command I am using is the following:

./SOAPdenovo all -s vite.config -K 31 -D 2 -F -o output_file -p 8

but I get the following error message:

all: invalid option -- F


Am I doing anything wrong? Moreover. I did not understand the differences between the -F flag and using the GapCloser software

thanks for your help

S

[stevebaeyen]

any news?

same problem here, the manual is very cryptic...

[stevebaeyen]

soapdenovo gapcloser

Hi guys I am experiencing some problem with the flag -F of SOAPdenovo. The command I am using is the following:

./SOAPdenovo all -s vite.config -K 31 -D 2 -F -o output_file -p 8

but I get the following error message:

all: invalid option -- F


Am I doing anything wrong? Moreover. I did not understand the differences between the -F flag and using the GapCloser software

thanks for your help

S

Hi, you have to follow the 4-step assembly of soapdenovo as described on the Soapdenovo website instead of using the all command. In the last step (scaffolding) you can enter the -F parameter and that's it! have fun !