Introduction

The FindJunctions program is a Java program that uses spliced alignments to identify and quantify exon-exon junctions in RNA-Seq data. When given a BAM file, it produces a BED file that summarizes every spliced aligned alignment identified in the BAM file. If also given a reference genomic sequence file (in .2bit format) it attempts to identify the strand of origin for each junction by looking for canonical intron splice junction sequences.

How to use FindJunctions

You can view FindJunctions by:

1. Zooming in on the gene or region of interest.
2. Click on Load Data.
3. Right-click on the track, and select Track Operations -> FindJunctions -> Use Default

Image Added

FindJunctions will appear as a new track. Brackets represent spice junctions across exons. Each bracket includes the number of reads supporting each splice junction.

In this example you can see that exclusion of the 5th exon is supported by nine reads.

 Image Added

The default behavior for FindJunctions is to identify split reads with a minimum of five basepairs on either side of the exon.

You can change this number by:

1. Right-clicking on the track, and select Track Operations -> FindJunctions -> Configure…
2. Inputting a new number.

How to get FindJunctions

To obtain a copy of FindJunction, you can either download a copy of the compiled "jar" file or get a copy of the source code and compile the program yourself.

...

To get a copy of the source code, check it out from the Genoviz repository and then use ant to compile it, as follows:

$ svn co http://svn.code.sf.net/p/genoviz/code/trunk/tools/FindJunctions
$ cd FindJunctions
$ ant release

...

To run the program from the command line, you would do something like:

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

...