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To run FindJunctions as a stand-alone program, visit https://bitbucket.org/lorainelab/findjunctions.

Follow the instructions there to compile FindJunctions and create a "jar" file using Apache Maven.

FindJunctions takes one argument, the name of a BAM file, and multiple options:

  • -u (unique) Ensures that only uniquely mapping spliced reads (with NH tag equal to 1) will be used to construct junctions. Default is to use all reads regardless of mapping quality or number of mappings obtained.
  • -n 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 Absolute path to a .2bit format genomic sequence file that will be used to identify junction strand. Required.
  • -o (output) Name of the junctions file that will be written. Default is print to stdout.

Output is tab-delimited BED12 format. The name field contains a name constructed from the location of the junction and the score field contains the number of spliced alignments supporting each junction. 

Example:

Code Block
java -Xmx1g -jar FindJunction_exe.jar -u -n 5 -b Genome.2bit -o FJ.bed sample1.bam,sample2.bam

Here, the -Xmx1g option specifies that the program can run with up to 1 Gb of computer memory (RAM) using the code in jar file (-jar) FindJunction_exe.jarrun it.