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-   -   Help with finding complementary sequences in ngs data (http://seqanswers.com/forums/showthread.php?t=12229)

Ami 06-22-2011 12:12 AM

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 :confused:.

Thanks,

Amit

StephaniePi83 04-02-2013 11:48 PM

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


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