Help with finding complementary sequences in ngs data

[Ami]

Hello everybody,

I am analyzing ngs data for small RNAs (18-30nt). I need to find out sequences which show complementarity for first 5-20 nt (from their 5' or 3' ends). I understand there are a lot of such sequences in my data set, after aligning them on to genome with Bowtie. I see many sequences that arise from plus strand, show overlap for 5-20 nt with the sequences arising from minus strand (complimentary). Please suggest me if there is any tool available to fish out this data .

Thanks,

Amit

[StephaniePi83]

Hi Ami,
did you find a tool able to do this ? I have the same thing to do !
Thanks.