View Single Post
Old 12-27-2014, 08:10 AM   #3
suhalsuhaimi
Junior Member
 
Location: US

Join Date: Dec 2014
Posts: 5
Default

Thank for you quick reply GenoMax. I already add your cmd like this:

aconty@aconty-VirtualBox:~$ echo `export PATH=$PATH:~/Desktop/BioTool/velvet` >> ~/.bashrc
aconty@aconty-VirtualBox:~$ chmod a+x velveth velvetg
aconty@aconty-VirtualBox:~$ ./velveth
aconty@aconty-VirtualBox:~$ ln -s /path/to/Desktop/BioTool/velvet/project/folder/J99.fasta
ln: failed to create symbolic link ‘./J99.fasta’: File exists
aconty@aconty-VirtualBox:~$ ln -s /path/to/Desktop/BioTool/velvet/project/J99.fasta
aconty@aconty-VirtualBox:~$ ln -s /path/to/Desktop/BioTool/velvet/project/HPAG1.fasta
aconty@aconty-VirtualBox:~$ ./velveth my_velvet_folder 21 -shortPaired data/J99.fa
aconty@aconty-VirtualBox:~$ ./velvetg
aconty@aconty-VirtualBox:~$ ./velvetg my_velvet_output
aconty@aconty-VirtualBox:~$ ./velveth my_velvet_output 35 -fasta -shortPaired -separate J99.fa HPAG1.fa
aconty@aconty-VirtualBox:~$ ./velvetg my_velvet_output -clean yes -exp_cov 21 -cov_cutoff 2.81 -min_contig_lgth 200

while i'm doing this. There is no feedback from SLUM and doesn't appear any basic held when I type ./velveth or ./velvetg

And the output folder that I want to create is my_velvet_output. I did not see this folder appear in my velvet file. When I create this output folder, it should appear in my velvet file, right? If i'm wrong, please correct me.

one more thing, why I cannot locate my fasta file into my velvet folder. Is there any other correct cmd tht I need to use?

Please help me....
suhalsuhaimi is offline   Reply With Quote