IGB User's Guide
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Follow the instructions to compile FindJunctions and create a "jar" file.

Then run Run the program using java, providing a comma-separated list of BAM files.

OptionsOptional options:

  • -u option (for unique) ensures that only uniquely mapping spliced reads (with NH tag equal to 1) will be used to construct junctions. 
  • -n option is the number of bases that must map to either side of a putative intron for a spliced read to be used to create or support a junction feature. Default is 5.
  • -b is the absolute full path to the .2bit genomic sequence file that will be used to identify junction strandstrand 
  • -o (output) is the name of the junctions file that will be written. 

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