The data can be found on the diabImmune website [https://pubs.broadinstitute.org/diabimmune/t1d-cohort]
We conducted analyses of the metagenomic data and subsets of the 16S data. The code used for these analyses can be found below
Mike and Natasha
#import the data
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path fastq_manifest.csv
--output-path diabimmune-demux.qza
--source-format PairedEndFastqManifestPhred33
#use dada2 for denoising
qiime dada2 denoise-paired
--i-demultiplexed-seqs paired-end-demux.qza
--p-trim-left-f 0
--p-trim-left-r 0
--p-trunc-len-f 0
--p-trunc-len-r 0
--o-table diabimmune_table.qza
--o-representative-sequences diabimmune_rep-seqs.qza
--o-denoising-stats denoising-stats.qza
#taxonomy analysis
qiime feature-classifier classify-sklearn
--i-classifier gg-13-8-99-515-806-nb-classifier.qza
--i-reads wanted_samples_rep_seqs.qza
--o-classification taxonomy.qza
qiime metadata tabulate
--m-input-file taxonomy.qza
--o-visualization taxonomy.qzv
qiime taxa barplot
--i-table wanted_samples_table.qza
--i-taxonomy taxonomy.qza
--m-metadata-file diabimmune_t1d_16s_metadata.txt
--o-visualization taxa-bar-plots.qzv
#generate a fasttree (we wouldn't use this in real life, but we were short on time at this point)
qiime alignment mafft
--i-sequences wanted_samples_rep_seqs.qza
--o-alignment aligned-rep-seqs.qza
qiime alignment mask
--i-alignment aligned-rep-seqs.qza
--o-masked-alignment masked-aligned-rep-seqs.qza
qiime phylogeny fasttree
--i-alignment masked-aligned-rep-seqs.qza
--o-tree unrooted-tree.qza
qiime phylogeny midpoint-root
--i-tree unrooted-tree.qza
--o-rooted-tree rooted-tree.qza