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-   -   SOAPdenovo flag -F (http://seqanswers.com/forums/showthread.php?t=6815)

scami 09-12-2010 10:43 PM

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

stevebaeyen 11-29-2011 07:16 AM

any news?
 
same problem here, the manual is very cryptic...

stevebaeyen 12-07-2011 12:08 PM

soapdenovo gapcloser
 
Quote:

Originally Posted by scami (Post 25123)
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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