FindJunctions is a Java program that uses spliced alignments to identify and quantify exon-exon junctions in RNA-Seq data.
When given one or more BAM files and a corresponding sequence file (in 2bit format), FindJunctions produces a BED file with junction features summarizing spliced alignments in the BAM file. The score field indicates the number of spliced alignments flanking each junction feature.
FindJunctions uses the sequence file to infer the direction of transcription for junction features.
This produces something similar to junctions.bed made by TopHat but with extra options.