Hello

I have:

Illumina sequences,50bp,~45M in fastq format

objective:

characterize KNOWN and NOVEL miRNA.

plan:

Align the reads against the reference genome using the bowtie aligner. All reads which align, will blastn against miRBase and Rfam sequences to identify KNOWN miRNAs. The reads which align but not match any known miRNA/RNA sequence will test by Mfold/ RNAfold for hairpin structure to characterize NOVEL miRNAs.

question:

what is the best bowtie parameters to use when annotating miRNA?

any advise to improve the annotation pipeline?

Thank you in advance...