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Old 03-25-2011, 06:04 AM   #1
nitinkumar
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Location: UK

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Post 454 Mapper

I want to do the sequencing based on reference genome using gsMapper. I know the commands, but I don't know how to analyse the results. Can any body help me in this???
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Old 03-25-2011, 10:47 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

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Post mapping analysis can take many forms. It depends on what you are looking for. We give our customers a whole bunch of files to work with and generally only "lightly" hold their hand as they ferret out the information that they want. In your case, I do not think that SeqAnswers will be able to help you unless you can more completely specify what you wish to find. Since you know gsMapper and can run the commands some initial starting thoughts include:

What files do you get back?
What further information are they missing so that you can get to your goal?
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Old 05-30-2011, 10:33 PM   #3
Jayu
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can anyone suggest how does gs mapper does internal triming??
Awaiting for the reply.
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Old 05-31-2011, 11:57 AM   #4
westerman
Rick Westerman
 
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Quote:
Originally Posted by Jayu View Post
can anyone suggest how does gs mapper does internal triming??
Awaiting for the reply.
I really don't understand the point of your question. Are you asking what algorithm it is using -- for such short matching probably S/W. Or are you asking what it takes into consideration -- this is probably just the quality values and adapter/vectors. Or perhaps you are asking about something more sophisticated?
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