Align sRNA reads from two libraries

[bornanarchist]

Hi All,

I need to check if there are some common reads between two sRNA libraries. In fact what I trying to do is find specified set miRNAs in my sRNA libraries. I know its wild to directly align both but I didn't had much luck with miRNA predicted from my sRNA library. Can anybody suggest me a good tool? Bowtie or Shrimp?

Thanks

B.A