I’m quite new in mothur and metagenomic thingy
I’d like to do a beta-diversity analysis using different datasets
The datasets using different sequencing platforms and different 16S region too. So i did the pre-processing steps separately for each dataset.
What should i do to analyze the beta-diversity measurement from those datasets? Is there any files (from processing steps) that I need to merge ?
Thank you in advance
Apart from doing this individually, since there is different regions involved, I do not think you ca reconcile the two. Unless you strictly use a taxonomic approach? I do not think you can do this in Mothur though.
Sorry I cannot be of more help.
As Alexandre mentioned, you could run everything through the phylotype pipeline and then make a comparison using mothur. But… I generally think mixing datasets - even if theyr’e the same region - is a bad idea since you’ll be combining different extraction methods, primer sets, etc and they aren’t an apples to apples comparison. Rather, I would run your analyses using each dataset separately and then compare the results like a traditional meta analysis.
Hope this helps,
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