I have miRNA-seq data (Single end) which I map to the whole UCSC hg19 genome. Now given the SAM output of this mapping, is there a way I can summarize the alignment over several genomic features:
- Mature miRNA
- precursor miRNA
- human Ribosomal RNA
- human5S rDNA
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 way to do it.