Question: Help with NGS analysis
1
gravatar for Nikky
3.7 years ago by
Nikky10
South Africa
Nikky10 wrote:

Hello everyone, I'm new here. I did the NGS of some of my forests soils samples. I have no idea how to analyze the data I got. Please help!

next-gen • 1.3k views
ADD COMMENTlink modified 2.7 years ago by joe.khulan0 • written 3.7 years ago by Nikky10
3

If you want to learn more about bioinformatics and analysis, you might take a look at the (in development) Biostars handbook

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Madelaine Gogol5.2k
2

Sounds like you could do with a collaborator. Where are you based? I'm sure there must be others at your institute that have experience with NGS.

ADD REPLYlink written 3.7 years ago by christopher medway440

your question is to broad. splease specify what type of ngs you do (rna-seq, genomic), and what you want to do with.

ADD REPLYlink written 3.7 years ago by romain.lannes80

Mi-seq illumina sequencing. I'm trying to study the biodiversity of ammonia oxidizing, phosphate solubilizing and nitrogen fixing bacteria in the forests soils

ADD REPLYlink written 3.7 years ago by Nikky10

what kind of NGS (technology, library, insert size, etc..)?

what is the question you are trying to answer?

how we can help if we do not know what you need or what you have!

ADD REPLYlink written 3.7 years ago by Medhat8.8k

Mi-seq illumina sequencing (16S rRNA gene V4 variable region). I am studying the biodiversity of ammonia oxidizing, phosphate solubilizing and nitrogen fixing bacteria in the soils.

ADD REPLYlink written 3.7 years ago by Nikky10

Reminds me of this (satirical) blog post.

In all seriousness, please consider things like this upfront. Try to get some public data before you start sequencing and think about what you are going to do with the data. Think ahead, not just step by step.

Furthermore, I agree with what has been said here before: get help and read a lot. If you have a specific question we would be glad to help, but something so broad as this is not something we can help with.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by WouterDeCoster44k
1

While this may be hard to comprehend for folks from developed parts of the world it is not uncommon for PhD mentors in developing countries to focus on an "in" technique and try to do "something" related to it. Since grad students do most of the work this falls on them without much choice. In such cases unfortunately the cart comes before the horse and the grad student is left to wrangle them together.

ADD REPLYlink written 3.7 years ago by genomax90k

Might be true, unfortunately. But given the wealth of public data available it's always possible to try and prepare yourself. Since we don't know their lab organisation/planning/... it's hard to speculate on that.

ADD REPLYlink written 3.7 years ago by WouterDeCoster44k

this will work if the student at least have some knowledge of what to do with it, or the supervisor give him a hint, but in case if neither he knows nor the supervisor guided him what do you expect?

ADD REPLYlink written 3.7 years ago by Medhat8.8k
3
gravatar for DG
3.7 years ago by
DG7.1k
DG7.1k wrote:

Honestly the best answer I can give you is to find a collaborator to help you out. While we on a forum can certainly answer lots of technical questions and point you in the right direction, the best way to learn something like this when you don't have any idea where to start, is to collaborate with someone if at all possible.

You should also be reading extensively from the literature. Metagenomics analysis of environmental samples is a huge field. There are tons of seminal papers in this field and lots of different programs out there. I can personally recommend software and pipelines developed by the Langille Metagenomics Lab and the iSEEM project from Jonathan Eisen's lab

ADD COMMENTlink written 3.7 years ago by DG7.1k
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