Bigwig To Wig Conversion

Question

[Dr.Bunsen]

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.

[arsala521]

Can you please share the link from where you installed bigWigToWig? Thank you

Answer 1

[Pierre Lindenbaum]

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

[Dr.Bunsen]

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.

[Pierre Lindenbaum]

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

[Byron Smith]

...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.

[Dr.Bunsen]

@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.

Answer 2

[Farhat]

It is possible bigwigtowig is not executable. Type

chmod +x ./bigWigToWig

and rerun your command.

[Dr.Bunsen]

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

[morteza.mahmoudisaber]

Also solved the problem for me

thanks a lot

[vinayjrao]

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

[Pierre Lindenbaum]

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

[vinayjrao]

platform and program are both 64 bits

Answer 3

[Byron Smith]

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).

[Dr.Bunsen]

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?