Hi people, I have a litle problem with Bowtie alignments. I am tryin to align 
sRNA Illumina dataset to hairpin mirbase. The problem is that after the steps 
(detailed below) I only obtain reads of 15-18nt, and I know that I have a lot 
of microRNAs (20-22nt) in my data. Beside the size problem, I realized that 
when the reads and the reference (the precursor in any case) the sequences 
don't match as I would expect.
The sequential steps that I've made:
- Groom
- Clip (adaptor elimination)
- Bowtie against hairpin database (mirBase precursor)
- SAM-to-BAM
- Download Bam and Bai files
- Open in IGV the file and the hairpin database

May be I am doing something really bad, but I dont know. Any 
Thanks in advance
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