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:
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.
- Unaligned
- Mature miRNA
- precursor miRNA
- piRNA
- lincRNA
- human Ribosomal RNA
- snoRNA
- human5S rDNA
- 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.
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