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Old 07-22-2013, 10:43 PM   #1
rjames
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Default Downstream Analysis

Hi, I want know about the basics of Downstream analysis, tools used in it and applications. If you please suggest some papers , articles or sites where i can find what i'm looking for.

Thanks!

RJames
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Old 07-22-2013, 10:48 PM   #2
chadn737
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You need to be A LOT more specific. Exactly what sort of "downstream analysis"?
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Old 07-23-2013, 02:09 AM   #3
rjames
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i just want to know the basics not specific. What is downsteam-anlysis? I have some single end ion torrent PGM 316 data in both fastaq and sff formats. I will start working on them within a month. i'm just collecting information and trying to know the basics first before starting my work.
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Old 07-23-2013, 02:47 AM   #4
dpryan
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Downstream analysis means any analysis done after some common step (the data/information flows "downstream" from the initial step). Normally this would be whatever is done after alignment, so it's too broad of a question to give a specific answer to.
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Old 07-23-2013, 04:01 AM   #5
GenoMax
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Here is a generic guide to get you started since you have not specifically said *what* kind of downstream analysis you are going to do.

http://en.wikibooks.org/wiki/Next_Ge...cing_%28NGS%29

There is a forum dedicated to Literature Watch on SeqAnswers that you may have already noticed: http://seqanswers.com/forums/forumdisplay.php?f=10

Recent Nature Biotechnology focus issue: http://www.nature.com/nbt/focus/sequ...012/index.html
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Old 07-23-2013, 04:35 AM   #6
rjames
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Thanks a lot. I will be working on single end reads obtained from Ion Torrent PGM 316. The DNA are of drug resistant strain of Stephaococcus aureus.
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Old 07-23-2013, 04:37 AM   #7
rjames
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Quote:
Originally Posted by GenoMax View Post
Here is a generic guide to get you started since you have not specifically said *what* kind of downstream analysis you are going to do.

http://en.wikibooks.org/wiki/Next_Ge...cing_%28NGS%29

There is a forum dedicated to Literature Watch on SeqAnswers that you may have already noticed: http://seqanswers.com/forums/forumdisplay.php?f=10

Recent Nature Biotechnology focus issue: http://www.nature.com/nbt/focus/sequ...012/index.html
Thanks a lot. I will be working on single end reads obtained from Ion Torrent PGM 316. The DNA(reads) are of drug resistant strain of Stephaococcus aureus.
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Old 07-23-2013, 05:53 AM   #8
rhinoceros
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It amazes how common the practice of pushing NGS data to people who have zero experience with it seems to be (based on reading this forum). I mean, sure you have to start somewhere.. but still..
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Old 07-23-2013, 07:13 AM   #9
Heisman
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Quote:
Originally Posted by rhinoceros View Post
It amazes how common the practice of pushing NGS data to people who have zero experience with it seems to be (based on reading this forum). I mean, sure you have to start somewhere.. but still..
In a previous lab we did a lot of collaborations and the people we collaborated with WANTED the data and thought they could handle it. They never could and we would end up helping/doing things for them. I think the issue is people underestimate the complexity of working through these datasets. Most general users don't even have the necessary computational power.
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Old 07-23-2013, 07:21 AM   #10
rhinoceros
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Quote:
Originally Posted by Heisman View Post
In a previous lab we did a lot of collaborations and the people we collaborated with WANTED the data and thought they could handle it. They never could and we would end up helping/doing things for them. I think the issue is people underestimate the complexity of working through these datasets. Most general users don't even have the necessary computational power.
When I started at my current job, there were quite a few people here who were handling NGS data manually line by line (say for example arranging 16S reads by length). As you can imagine, things progressed very very slowly
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