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Old 06-22-2011, 12:12 AM   #1
Ami
Junior Member
 
Location: Singapore

Join Date: Aug 2010
Posts: 6
Default Help with finding complementary sequences in ngs data

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
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