Diversity changes within an environmental sample at different conditions

Hello all,
I am new user and have no background of bioinformatics or microbiome analysis so the questions might be very basic.
I have Illumina 16s paired end sequences for an environmental sample V3-V4. I want to study change in diversity with change in pH. I have enriched the sample in different pH conditions and Now I want to compare it to the native.
What pipeline should I follow? or what all are the analysis that can be done.

I am following the Qiime 2 workshop as a free viewer, But I also would like to know more specific to my data set.

Thank you.

Hi @sakshi,

For me, this is a super advanced and complex question! At many places I’ve worked, these kinds of discussions with a bioinformatician or biostatistician actually warrant authorship on the manuscript because it’s a piece of experimental design and a pretty substantial contribution. Choosing pipelines means shaping your data, outcomes, and options. Others may have different feeelings here, but that’s my two cents.

There are many approaches, and the tutorial provides one pipeline that a lot of people find useful and follow. There are other approaches with other motivations, too. I would also recommend thinking through your data type and which tests are appropriate for which type of that. (There’s some discussion on here about this type of thing you may find useful :slight_smile: ).



Thank you so much for the reply. That is very fair that this might amount to authorship. Although, I do not have a problem with that. I am very new to the field and am genuinely trying to understand. If anybody can help me with it my supervisor and I will have no problem in giving authorship.
PS: I am trying to read and understand more so that I can do it myself too. :slight_smile:

Thank you,