trouble with twoBitToFa command

[Ayushi Jain Phd. 2015]

Hello

I am using your "twoBitToFa" utility to convert rat genome sequence into fasta format on a linux.x86_64 system. I have downloaded it from your website and I am getting the usage statement in the linux terminal but the command is still not working.

I am using the command as follows:

twoBitToFa rn6.2bit genome.fa

but the system shows the message "command not found". I have tried changing permissions using chmod command, even tried ./twoBitToFa  as well as suggested on your "2bit extraction" google group but nothing seems to work.

Please suggest me the needful.

Thank you

Ayushi Jain

c/o Dr. Subeer Majumdar

Cellular Endocrinology Laboratory

National Institute of Immunology

New Delhi

[Jairo Navarro Gonzalez]

Hello Ayushi,

Thank you for using the UCSC Genome Browser and your inquiry.

If the directory containing the twoBitToFa utility is not defined inside of your PATH variable, you will have to specify the location of the tool before your system can run the program. For example, if your current working directory contains the twoBitToFa utility, then you can execute the utility by using the command you shared:

$ ./twoBitToFa rn6.2bit genome.fa

If the twoBitToFa utility is in a different directory (not the same directory as rn6.2bit and genome.fa) then you will need to use the full path to the directory that contains twoBitToFa. If that still doesn't work, please run these commands in the directory that contains twoBitToFa and send us the results:

$ pwd

$ ls -l twoBitToFa

$ file twoBitToFa

A quick way to verify if the utility is defined in your PATH variable is to use the "which" command, i.e.,

$ which twoBitToFa

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genome Browser

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