Jonathan A. Eisen edited Methods.md  over 9 years ago

Commit id: 3145558c6b50ad8b5e8749f04a9afd4c579f3d1f

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##Bioinformatic Analysis  Demultiplex, QIIME, blah,blah, blah  ###OTU assignment and QC  The number of high-quality sequences per sample ranged from 26830 to 77845 (see Table X). The pick\_open\_reference\_otus.py script (CITATION OR LINK?)  was used to cluster sequences at 97% similarity. Taxonomy was assigned to each cluster by comparing a representative sequence from each cluster to the gg\_13\_8\_otus reference taxonomy provided by the Greengenes Database Consortium (http://greengenes.secondgenome.com.) No chimeric sequences were identified using the identify\_chimeric\_seqs.py script and there were no singleton OTUs (probably should verify these things). All subsequent beta diversity analyses (comparisons across samples) were performed with all samples rarefied to 26830 sequences. ###Comparison of ISS surfaces to analogous surfaces in homes on Earth  The sequences and associated metadata from the Wildlife of Our Homes Project are available for download from Figshare \cite{885e3742-e0c3-4719-a6a8-dba9930a33ca}. These were used in a combined analysis with the ISS sequences presented here. Because the sequences from the two projects are of different lengths, each dataset was independently analyzed using a closed-reference OTU-picking approach, and the resultant biom tables were merged with the merge\_otu\_tables.py script.