Introduction

The FindJunctions program is a Java program that uses spliced alignments to identify 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 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 download a compiled copy, click

A version of the FindJunction program corresponding to revision 14387 of the GenoViz source code repository is attached to this wiki page.

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
$ cd tools/FindJunctions

This will create a new file named dist/FindJunction_exe.jar. Use this file to run the program.

Using the jar file to run FindJunction

A version of the FindJunctions program corresponding to revision 14387 of the GenoViz source code repository is attached to this wiki page. To run the program from the command line, you would do something like:

java -Xmx1g -jar FindJunctions_exe.jar -u -n 5 -b Genome.2bit -o FJ.bed sample.bam

In this example,