Question: Bigwig To Wig Conversion
1
gravatar for Dr.Bunsen
7.8 years ago by
Dr.Bunsen140
Dr.Bunsen140 wrote:

Hello, I am trying to convert a bigWig file to a Wig file. Does anyone know how to do this?

I am trying to use the bigWigToWig program from UCSC. From the command line I have tried:

bigWigToWig in.bigWig out.wig

Unfortuantely, this command give me this error:

bigWigToWig: command not found

I have the bigWigToWig program as well as the in.bigWig file in the same directory. Does anyone have a solution or know what I am doing wrong?

Thanks in advance for the help.

bigwig ucsc • 13k views
ADD COMMENTlink written 7.8 years ago by Dr.Bunsen140
4
gravatar for Pierre Lindenbaum
7.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

under linux check that the folder containing bigWigToWig is in your $PATH

export PATH=${PATH}:/your/path/to/ucsc/bin
bigWigToWig in.bigWig out.wig

or , as bigWigToWig is in your directory , you can just write

./bigWigToWig in.bigWig out.wig
ADD COMMENTlink written 7.8 years ago by Pierre Lindenbaum119k

Pierre, thanks for the help! I read the links you provided and followed your directions. I confirmed that the bigWigToWig program is now in my $PATH. When I now try to execute the bigWigToWig in.bigWig out.wig command, I get a Permissions denied error. I tried this locally on my Mac and also on our server. I get the same error. Any other ideas? Thanks again.

ADD REPLYlink written 7.8 years ago by Dr.Bunsen140

do you have the right to write here ? try "bigWigToWig in.bigWig /tmp/out.wig"

ADD REPLYlink written 7.8 years ago by Pierre Lindenbaum119k

...or try moving (copying) bigWigToWig into whatever directory the files you want to convert are located. Not a good permanent fix, but might work in the short term.

ADD REPLYlink written 7.8 years ago by Byron Smith30

@Pierre I tried your "bigWigToWig in.bigWig /tmp/out.wig" command and I also get a Permission denied message. I tried to run bigWigToWig on my local machine's Desktop rather than on the server and I still get the same Permission denied message?! I also double checked to make sure that bigWigToWig is in my path. Do you have any other ideas? Thanks again for all the help.

ADD REPLYlink written 7.8 years ago by Dr.Bunsen140
3
gravatar for Farhat
7.8 years ago by
Farhat2.9k
Pune, India
Farhat2.9k wrote:

It is possible bigwigtowig is not executable. Type

chmod +x ./bigWigToWig

and rerun your command.

ADD COMMENTlink written 7.8 years ago by Farhat2.9k
1

Thank you! This turned out to be the real problem.

ADD REPLYlink written 7.8 years ago by Dr.Bunsen140

Also solved the problem for me

thanks a lot

ADD REPLYlink written 3.3 years ago by morteza.mahmoudisaber70

Dear Farhat,

I tried doing the same, but my problem is that the file is a binary and therefore not an executable

The roor message that I get is - bash: ./bigWigToWig: cannot execute binary file: Exec format error

Thanks

ADD REPLYlink written 23 months ago by vinayjrao110

check your platform 32/64 bits vs the program 32/64 bits

ADD REPLYlink written 23 months ago by Pierre Lindenbaum119k

platform and program are both 64 bits

ADD REPLYlink written 22 months ago by vinayjrao110
2
gravatar for Byron Smith
7.8 years ago by
Byron Smith30
United States
Byron Smith30 wrote:

Assuming you're using linux:

Are you currently in the directory that has bigWigToWig in it? If so, and if it's not in your $PATH, you should use "./bigWigToWig". If you want to be able to run it without that './' move it to your $PATH or add it's directory to your $PATH (see Pierre's answer).

ADD COMMENTlink written 7.8 years ago by Byron Smith30

Byron, thank you for the help. Yes, the program (bigWigToWig) and the .bigWig file were initially in the same directory, so I tried your ./bigWigToWig suggestion. It returned a Permissions denied error (see above). Thanks for the help. Do you have any other suggestions?

ADD REPLYlink written 7.8 years ago by Dr.Bunsen140
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