Tweet
GapCloser using SOAPdenovo
Hey everyone!
I'm a rookie in these bioinformatics things.
I've been running my first genome assembly during these last couple of days and everything's fine using SOAPdenovo so far (at least i think so) - Unix (Linux)
After the assembly I used GapCloser tool with this command:
/nfs/m7/pcaldas/patiriella/GapCloser -b soap.config -a pcaldas.scafSeq -o pcaldas.scafSeqFILLED -t 8
but nothing happened!after a while running the scafseqFILLED (the file where's supposed to be the 'corrected' scaffolds) is empty and there's no error message or whatsoever.
I can't understand what i'm doing wrong but it's possible some rookie mistake.
Did I give you enough detail to have some help?
Thank you in advance.
I'm a rookie in these bioinformatics things.
I've been running my first genome assembly during these last couple of days and everything's fine using SOAPdenovo so far (at least i think so) - Unix (Linux)
After the assembly I used GapCloser tool with this command:
/nfs/m7/pcaldas/patiriella/GapCloser -b soap.config -a pcaldas.scafSeq -o pcaldas.scafSeqFILLED -t 8
but nothing happened!after a while running the scafseqFILLED (the file where's supposed to be the 'corrected' scaffolds) is empty and there's no error message or whatsoever.
I can't understand what i'm doing wrong but it's possible some rookie mistake.
Did I give you enough detail to have some help?
Thank you in advance.