Exploring Figshare

Today I’m uploading data to Figshare for the first time – getting our PhyloSift analysis published before we submit the manuscript.

On Edhar, the final data folders are qiime_analyses_yatsunenko_16S_amplicons and qiime_analyses_yatsunenko_metagenomes_7Oct. Figured this out after I looked through my e-mails from October (when I was running these analyses):

So I spent the weekend looking through yatsunenko data after my discovery about QIIME’s reference-based OTU picking protocol. It turns out that our 16S data is OK (this was a closed-reference based process, where all the reads not matchging greengenes were discarded), but the 16S derived from PhyloSift metagenome analysis was an open-ref process (where QIIME created new de novo clusters for sequences that didn’t match greengenes–e.g. opposite of what yatsunenko did).
 
Because I wanted to keep things consistent in the manuscript (keeping amplicon and metagenome workflows the same, and directly comparable with the Yatsunenko methods), I re-ran the metagenome data now using a Closed-Reference OTU picking process. That means we have a lot less OTUS, and might see different patterns in the PCoAs. Sorry about the confusion over this, just glad I caught it early enough.
 
New data has been downloaded to Edhar: /home/hollybik/yatsunenko_QIIME/qiime_analyses_yatsunenko_metagenomes_7oct
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