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Old 06-04-2011, 03:28 PM   #1
brc458
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Question What is a next generation sequencing technique and what is a NGS platform.

What is next generation sequencing: and the different techniques and platforms that are available

Last edited by brc458; 06-15-2011 at 12:34 PM.
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Old 06-04-2011, 06:21 PM   #2
shurjo
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Try starting here. Let me know if you cant get the full article and I will send you a copy.
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Old 06-04-2011, 11:26 PM   #3
brc458
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Shurjo,
Thank you. But what does it mean by techniques? Is that the same as platforms? Or does it refer to transcriptome, exome whole genome sequencing? The two terms are confusing me. I've written about the 458 and illumina so am assuming that i've written about "platforms" but what does it mean by techniques?
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Old 06-05-2011, 01:58 PM   #4
krobison
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I'd guess you've guessed right on techniques; experimental paradigms would have been the fancier & perhaps less ambiguous way to state it.
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Old 06-05-2011, 02:12 PM   #5
shurjo
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Quote:
Originally Posted by brc458 View Post
Shurjo,
Thank you. But what does it mean by techniques? Is that the same as platforms? Or does it refer to transcriptome, exome whole genome sequencing? The two terms are confusing me. I've written about the 458 and illumina so am assuming that i've written about "platforms" but what does it mean by techniques?
Each "platform" (Illumina/Solid/454/PacBio) can be used for multiple "techniques" (whole-genome/exome/transcriptome/ChipSeq/custom application). An analogous word sometimes used for "platform" is "chemistry".
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Old 06-06-2011, 05:47 AM   #6
charltt
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Quote:
Originally Posted by shurjo View Post
Try starting here. Let me know if you cant get the full article and I will send you a copy.
I'm an undergrad who is just beginning to explore bioiformatics. I tried the link above and I couldn't access the full text. Any chance you could email me a copy? Many thanks shurjo!
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Old 06-06-2011, 10:09 AM   #7
shurjo
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Quote:
Originally Posted by charltt View Post
I'm an undergrad who is just beginning to explore bioiformatics. I tried the link above and I couldn't access the full text. Any chance you could email me a copy? Many thanks shurjo!
Sure, pm me your email ID.
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Old 06-10-2011, 04:49 AM   #8
aforntacc
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I am new to this forum and as well a new fellow just trying to gain a PhD, my first task is to analyse a deep sequencing (Illumina) data from RNA of apple. how do i start? what should i do?
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Old 06-10-2011, 12:34 PM   #9
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Depends on your project and source of the RNA. Since it is RNA I am presuming you are doing a transcriptome project. Furthermore I am going to presume that you are looking for de-novo transcripts (as versus RNA-seq counts.) I do not know the state of the Apple annotation but, presuming that it is non-existent, then doing a cDNA assembly followed by an annotation program such as Blast2Go would be a good first start.

But I could be way off-base on the goals of your project. Why don't you describe it more fully and then people may be able to give you more concrete advice. To put this in other terms, basically what you asked us is akin to saying "I am visiting Rome; what should I do and where should I stay?" The answer is "it depends" -- unless we know more about what you want to accomplish.
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Old 06-11-2011, 11:02 PM   #10
camei
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I can't read the article recommended by shurjo neither. Can someone / you send me a copy also ? thx
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Old 06-15-2011, 09:17 AM   #11
ssvictor
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attached is the article that was requested
Attached Files
File Type: pdf NGS_overall.pdf (1.95 MB, 60 views)
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