How do get additional bam statistics

Question

[t-jim]

I have multiple bam files and I'm looking for some statistics about them.

I know how to generate basic statistics using samtools flagstat but i want additional statistics like how many reads are mapped to transcripts, to introns, to intergenic regions, etc.

Can someone tell me a way do do that?

[GenoMax]

• Picard's CollectRnaSeqMetrics (search for that word).
• RNA-SeQC is another