You can already load a GFF file in IGV

undefined

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;

undefined

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