TDF to bed graph -- IGV on command line
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8 weeks ago
a_bis ▴ 30

Hi all, I'm trying to convert some TDF files to bedgraph files so that I can do a genomic leftover on them (as far as I can tell, I can't lift over TDF files). This google group answer here (https://groups.google.com/g/igv-help/c/RcZw5YB5SOQ) says I can run igvtools on the command line and convert a TDF file to a bedgraph (this command can't be run through the GUI), and then proceed from there. However, I'm having a hard time running the command on the command line. I'm in a directory that contains both a version of IGV as well as the .tdf file that I want to convert to .bedgraph. When I run

igvtools tdftobedgraph input.tdf output.bedgraph


I get a

-bash: igvtools: command not found


message.

I also tried the following:

   java -Xmx1500m --module-path=lib @igv.args --module=org.igv/org.broad.igv.tools.IgvTools tdftobedgraph GSM1782914_Smad2_3_D3EB_AC_E14.tdf GSM1782914_Smad2_3_D3EB_AC_E14.bedgraph

Unrecognized option: --module-path=lib
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.


Could anybody advise on what exactly I should do to get IGV to run on the command line successfully? Thanks in advance!

tdf igv • 279 views
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This looks like the classic $PATH problem. If you are in the IGV install directory you may simply need to do ./igvtools and/or add the directory to your $PATH.

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Hi GenoMax, many thanks for the reply. I'm not in the install directory (I'm not sure where it is -- is it most likely the Applications directory where new downloaded apps are generally automatically installed?), but in a directory I made where I moved the IGV app and the relevant .tdf files. I'm not sure how to go about finding the install directory -- sorry to bug you again, but if you could give me a pointer as to how to how to find the install directory and add it to the \$PATH, I'd be very grateful!

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(I also tried running ./igvtools [command] [input] [output] and it gave me the same error message!)