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.