Too few aligments using Bowtie

[raulcruz]

I have using Bowtie to align short reads microRNA against the index m_musculus_ncbi37. The problem is that surprisingly few of them can be aligned perfectly (3%) or with 1 mismatch (10%). This percentages are much lower than what I have seen in other papers.

Here you have an example of the command options that I have been using:

./bowtie -c --tryhard -v 0 m_musculus_ncbi37 GTATGCCGTCTTCTGCTTGAAAAAAA

The result is:

# reads processed: 1
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments

Does anybody see anything wrong with the command? anything else that I need to check?

Thanks.