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Often times people will only get back a fasta file or they may get back the fasta and qual files.You really need the sff file or at least the fasta, qual, and flow file data.We picked the V35 region because we liked these primers the best for the types of samples that we generally process (i.e. You may choose to use another region based on the expected biodiversity of your samples.Second, this set of barcodes will allow us to simultaneously sequence 96 samples.A priori, we dedicate two of these barcodes to controls.The first is for resequencing a mock community made up of a defined consortia of 16S r RNA gene sequences where we know the true sequence.To that end we collected fresh feces from mice on a daily basis for 365 days post weaning (we're accepting applications).During the first 150 days post weaning (dpw), nothing was done to our mice except allow them to eat, get fat, and be merry.
starting at the 3' end of the V5 region, we sequence back towards the 5' end of the V3 region.
We were curious whether the rapid change in weight observed during the first 10 dpw affected the stability microbiome compared to the microbiome observed between days 140 and 150.
We will address this question in this tutorial using a combination of OTU, phylotype, and phylogenetic methods.
Starting out we need to first determine, what was our question?
The Schloss lab is interested in understanding the effect of normal variation in the gut microbiome on host health.