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Old 09-12-2010, 10:43 PM   #1
scami
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Location: italy

Join Date: Sep 2010
Posts: 55
Default SOAPdenovo flag -F

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
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Old 11-29-2011, 07:16 AM   #2
stevebaeyen
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Location: Belgium

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Default any news?

same problem here, the manual is very cryptic...
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Old 12-07-2011, 12:08 PM   #3
stevebaeyen
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Location: Belgium

Join Date: Aug 2011
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Wink soapdenovo gapcloser

Quote:
Originally Posted by scami View Post
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 !
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