Obtaining genomic features from miRNA-seq data based on UCSC hg19 alignment results

[foolishbrat]

I have miRNA-seq data (single end) which I map to the whole UCSC hg19 genome. Now given the SAM output of this mapping, what's the good pipeline to summarize that alignment so that I can get statistics of these genomic features:

1. Unaligned
2. Mature miRNA
3. precursor miRNA
4. piRNA
5. lincRNA
6. human Ribosomal RNA
7. snoRNA
8. human5S rDNA
9. snRNA

Namely for each of the above features how many of my reads (or percentage) are aligned?

I know CLC-BIO or Illumina inbox software possibly already have that. But I'm looking for noncommercial and tweakable/modular way to do it.

[TiborNagy]

Try the UEA Small RNA Workbench.