best way to compute how many reads map to non-coding regions?

[PFS]

I would like to estimate
1) how many reads map to non-coding regions
2) how many bases in non-coding regions are covered by at least one read.

I have RNA-Seq alignments.
Thanks!

[Simon Anders]

If you know a bit of Python, you can do this with a script of only a few lines with HTSeq by modifying the examples given in the HTSeq Tour.

[swbarnes2]

I'd try BEDTools. Make a .bed of coding regions, and then intersectBed will give you a filtered bam consisting of all the reads that don't hit your .bed file features. CoverageBed might help you count coverage of those regions.