Downstream Analysis

[rjames]

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

[chadn737]

You need to be A LOT more specific. Exactly what sort of "downstream analysis"?

[rjames]

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.

[dpryan]

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.

[GenoMax]

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_Generation_Sequencing_%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

[rjames]

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.

[rjames]

thanks

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_Generation_Sequencing_%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.

[rhinoceros]

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..

[Heisman]

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.

[rhinoceros]

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