How to count the splice junction mapping reads

Alignment of reads to the reference genome is usually the first step in the of RNA-Seq analysis of model organisms. Currently available RNA-Seq read alignment programs such as TopHat, STAR and Jaguar generate alignment in BAM format that also contains alignment for reads that span splice-junctions (containing introns as large alignment gaps). Splice-junction reads are important for the transcript assembly and expression as well as discovery of novel splice-junctions. Counting the number of splice-junction reads present in the sequencing library may indicate the overall data quality and transcriptome coverage. For a typical good quality sequencing library of a mammalian transcriptome 20-30% of the reads may correspond to the splice junctions (this is just and observation from the several RNA-Seq papers. True proportion might be much higher).
One simple way to count the number of splice-junction reads is to scan the alignment BAM file and select the count the read-aligments that contain "N" (skipped-bases") in the CIGAR string. These are the alignments that have skipped-bases from the reference genome (most likely introns in case of RNA-Seq reads). One may wish to exclude alignments wit the small deletios (such as 1N or 2N).

I've written a small wrapper script that first uses BamUtil's  findCigar program to extarct the splice-junction alignments and writes them in a BAM file.  The BAM file is sorted and then Picard tools' CollectAlignmentSummaryMetrics program is used to count the number of reads. The sctipt is available on our lab's website.