smallRNA: how analyze

[edeka]

Hello!
I am new to smallRNA seq and I am a bit confused as to analyze my data (from human genome).
it is better to:
1) align against ncRNA transcriptome from Ensembl
2) align against genome
3) aling against miRNA transcript, take the unaligned reads, align them against genome and after that annotate them with gtf file.

Or are there better options?

Thank you in advance
Best

[sbarberan]

I found that when exploring new data CAP-miRSeq is really helpful:

http://bioinformaticstools.mayo.edu/research/cap-mirseq/