How to convert TDF to bedgraph using igvtools with the IGV interface?

Question

[pb]

Hello, I want to convert a TDF to bedgraph using igvtools with the IGV interface. From the tools option, this is not available. Any help?

Answer 1

[GenoMax]

You will need to do this on the command line (terminal). See --> Conversion from tdf to bed format

[pb]

Hello, I`ve tried this but it always gives me an error message saying:

Lmod has detected the following error: The following module(s) are unknown:
"IGVTools"
Please check the spelling or version number. Also try "module spider ..."
It is also possible your cache file is out-of-date; it may help to try:
  $ module --ignore-cache load "IGVTools"

I`ve double checked the spelling and the capitalization and it looks fine. This was why I was hoping to use the IGV Interface instead...

[GenoMax]

Looks like you are using modules system for software. Is module for IGV not installed properly? What do you see when you try which igvtools after loading the module for igv?

[pb]

It says that IGVTools does not exist in my folder. I redownloaded the command line from the website (https://software.broadinstitute.org/software/igv/download) but it still did not work. Any more tips?

[GenoMax]

Download from here: https://software.broadinstitute.org/software/igv/download and then use https://software.broadinstitute.org/software/igv/igvtools_commandline

[ATpoint]

IGVtools is not IGV, it's two separate tool/toolkits.