When do you need them and are you likely to need more in the future?

We used the TruSeq whole exome kits, though we plan to switch to Agilent.  
Currently using Agilent's Kinome kit, would have them available.  

Agilent give substantial volume discount

Richard B. Everson, MD, MPH
Deputy Director for Cancer Prevention and Control
Carole and Ray Neag Comprehensive Cancer Center
University of Connecticut Health Center
263 Farmington Ave  MC 1628
Farmington, Connecticut 06030-2875
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-----Original Message-----
From: galaxy-user-boun...@lists.bx.psu.edu 
[mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Zhiqiang Shu
Sent: Monday, November 26, 2012 3:29 PM
To: Peter Cock
Cc: Galaxy-user
Subject: Re: [galaxy-user] Find out sense and antisense sequences

Thank you, Peter! I think I should put more detailed information here.

What I'm doing is piRNA data. Two groups of piRNA (named sense and 
antisense)are in the library. As I said, they are complementary to each other 
for about 10 nt, while the whole length is about 30nt. For the sense group, 
they share the feature of having an "A" at their 10th.

In this case, how can I deal with it? One possible way come up is inverting all 
sequences and aligning them.

Thanks!
Best,
Zhiqiang


Quoting "Peter Cock" <p.j.a.c...@googlemail.com>:

> On Mon, Nov 26, 2012 at 6:47 PM, Zhiqiang Shu <z...@bio.fsu.edu> wrote:
>> Hi, Galaxy users!
>>
>> I have a question on how to find out sense and antisense sequence. 
>> I've got RNA seq data in the fastq format. The sequences inside are 
>> partially complementary to each other (complementary is 10nt, while 
>> entire is about 30nt). How can I separate these sequences into two 
>> groups: sense and antisense
>
> Depending on how your sequences were prepared, you might be able to 
> look for a poly-A tail as a clue to orientation. Another approach is 
> to compare the (assembled) transcripts to known genes and if you only 
> get matches on one strand that is probably the correct orientation.
>
>> (one thing I know is for the sense sequence the 10th nucleotide is 
>> always "A")?
>
> Why is that? Is this related to your library preparation?
>
> Peter
>
>



--------------------------
Zhiqiang Shu/Deng Lab
Department of Biological Science
Florida State University
319 Stadium Dr.
Tallahassee, FL, USA, 32306-4295
z...@bio.fsu.edu


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