mothur

Comparison studies on amplicon sequence data

Dear Mothur users

Greetings

I would like to do a comparison studies with my amplicon sequence data with previously published data in a specific habitat. I am facing two hurdles. 1. I have generated my sequence data using 16S V3-V4 primers, but some of the previously published data have been generated by using different sets of primer’s like V4-V5, and V1-V2. In this case, is there is a way to analyse the data using mothur? 2. Further, i was re analyzing the data each time from the beginning, while adding new set of samples. Is there a way to circumnavigate my approach.

Many thanks
Venkat

Hi,

Unfortunately, you cannot cluster them together. One possibility would be to classify everything together at the genus level, but the problem with that is that not all regions classify equally well. I’d suggest processing the datasets separately, and then comparing the results across studies. We have done this with papers reporting obesity and microbiome data to perform a meta-analysis. I suspect you could do the same thing for your habitat. Here’s the publication where we did it…

Pat

Dear Dr. schloss

Thank you for your suggestions and the article.

Venkat

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