Hello Everybody,
I want to learn NGS data analysis especially of Human Gut microbiome. Can anybody suggest me what I should to learn from the very beginning as I have no experience to analyze NGS data.or any step by step protocol/guidelines to learn?
Mati
Hi Mati,
Kindly see the attached article below, to understand the microbiome analyses.
And further to start analyzing, here is the link of Qiime tutorial for the step by step analysis, scripts and outcomes.
http://qiime.org/tutorials/tutorial.html
Hopefully it will help,
All the best!
Dear Mati,
QIIME is a pipeline which has extensive support and community inputs (qiime google forum) and its great. I am not aware from which part of analysis you would want answers to this question. So, I wish to put forward certain points. QIIME uses python, so what ever commands you are running are all python scripts clubbed together in the forms of a pipeline. Its a complete package, from informatics to statistics, all in one platform.
There is another platform from Robert Edgar, the UPARSE pipeline (www.drive5.com) which is also great.
Processing microbiome sequence data wont be problematic whichever pipeline you choose, but the important part is statistical inference. Multivariate analysis and coming to some conclusion. Microbiome is purely ecology. Questioning ecology and answering ecology (100 fundamental ecology questions). So the importance is to handling the processed data. For that I would suggest multivariate analysis of ecological data and biplots in practice (link below) from Prof Greenacre.
Coming to relevance in human microbiome studies you should follow walkthroughs from the HMP-DACC (http://www.hmpdacc.org/resources/tools_protocols.php). This is an immense resource.
http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12025/abstract
http://www.multivariatestatistics.org/biplots.html
http://www.multivariatestatistics.org/maed.html