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 help/suggestion/tip?
Thanks in advance