Getting SignalMap GFF files into IGV

You can already load a GFF file in IGV

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This will allow you to load your file into IGV, however it will be slow especially for many tracks. So you may wish to convert the GFF to a bedgraph file, and then from there create a TDF file.

Convert GFF into a bedgraph file

cat input.gff | awk '{print $1"\t"$4-1"\t"$5"\t"$6}' > output.bed

and then convert this bed file to a TDF file which can be done using igvtIGV. 

In IGV, go to the 'Tools' -> 'Run igvtools' menu at the top and you will get the following box;

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Ensure the 'Command' is set to "toTDF", set the 'Input File' to your bedfile, the 'Output File' will be filled in automagically (unless you want to change it) and then set the 'Zoom Levels' to 10.

This will create a new tdf file which is much smaller than the bedfile and contains the histogram you would have had in SignalMap.

NOTE: Still to write up

  • Give visuals of signal map/IGV
  • Command-line method of doing this

 

Installing Roche SignalMap on Windows 10

 

In our lab we sometimes use a piece of software called SignalMap by Roche to visualise the outputs from some legacy pipelines. This is a very simply GFF viewer which displays the score column (the 6th column) of a GFF file as a histogram. It will also display regular GFF features such as genes, transposons etc. quite nicely. 

Despite it being a tidy little program it does not appear to have been updated for quite a while (2013 maybe as that is the date on the copyright). Needless to say there hasn't been an update since Windows 10 was released in 2015. If you simply try to run the SignalMap installer exe file you get a bunch of errors. Since we use this software, everyone is used to it and until it becomes 100% necessary to have to ditch it for bedgraph files in IGV (maybe more in another post) then I need to get this to work.

Here was my workaround;

After installing the Java Runtime Environment (JRE) and then downloading the SignalMap you need to break out your Windows command-line and then type the following;

C:\Users\USER\Desktop> SignalMap_installer.exe LAX_VM "C:\Program Files (x86)\Java\jre1.8.0_101\bin\java.exe" -i GUI

This works under the following assumptions;

  • That the SignalMap_installer.exe file is downloaded to your Desktop and the current working directory is the Desktop directory.
  • The java.exe file is located here, but obviously if you have installed a different version of JRE then it's quite likely the directory will differ slightly (probably just the version number)

Once you've taken those two assumptions into account to run that command the installer will start and you can proceed as normal.

NOTE:

This method does have the implication that it fixes SignalMap to a specific version of the JRE which would mean that if a new version of JRE is installed, e.g. with security patches, then there could be a risk. The user in me doesn't care, I just want to look at the pretty histograms in my BS-Seq data, but the Sys-Admin in me hates it and would never deploy it on a shared system. The world of Bioinformatics and Scientific computing....ENJOY!

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