TITLE: No Title
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[DESCRIPTION]
<p>Commands for hands-on component for Qiime are found in guidelines.</p>

[GUIDELINES]
<p><strong>1. Checking mapping file format</strong></p>
<p> </p>
<div data-canvas-width="149.19595927068002">$ validate_mapping_file.py -m map_file.txt -o mapping_file_output</div>
<div data-canvas-width="149.19595927068002"> </div>
<div data-canvas-width="149.19595927068002"><strong>2.1 Join paired end reads</strong></div>
<div data-canvas-width="149.19595927068002"> </div>
<div data-canvas-width="149.19595927068002">
<div data-canvas-width="315.5612411589749">$ join_paired_ends.py -f Undetermined_S0_L001_R1_001.fastq -r Undetermined_S0_L001_R2_001.fastq -b Undetermined_S0_L001_I1_001.fastq -o reads</div>
<div data-canvas-width="315.5612411589749"> </div>
<div data-canvas-width="315.5612411589749"><strong>2.2 Depmultiplex &amp; quality filter</strong></div>
<div data-canvas-width="315.5612411589749"> </div>
<div data-canvas-width="315.5612411589749">
<div data-canvas-width="222.4794897879751">$ split_libraries_fastq.py -i fastqjoin.join.fastq -b fastqjoin.join_barcodes.fastq -o split -m map_file.txt -q 29 --barcode_type 12 --store_demultiplexed_fastq</div>
<div data-canvas-width="222.4794897879751"> </div>
<div data-canvas-width="222.4794897879751"><strong>3.1 <em>De novo </em>OTU picking</strong></div>
<div data-canvas-width="222.4794897879751"> </div>
<div data-canvas-width="222.4794897879751">
<div data-canvas-width="277.5732852564001">$ pick_de_novo_otus.py -i subs_seqs_q.fasta -o uclust_otus/</div>
<div data-canvas-width="277.5732852564001"> </div>
<div data-canvas-width="277.5732852564001"><strong>3.2 Closed-reference OTU picking</strong></div>
<div data-canvas-width="277.5732852564001"> </div>
<div data-canvas-width="277.5732852564001">
<div data-canvas-width="268.93276898197496">$ pick_closed_reference_otus.py -i subs_seqs_q.fasta -r $PWD/gg_13_8_otus/rep_set/97_otus.fasta -t $PWD/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt -o_ref_otus</div>
<div data-canvas-width="268.93276898197496"> </div>
<div data-canvas-width="268.93276898197496"><strong>3.3 Open-reference OTU picking</strong></div>
<div data-canvas-width="268.93276898197496"> </div>
<div data-canvas-width="268.93276898197496">
<div data-canvas-width="261.58773669274274">$ pick_open_reference_otus.py -i subs_seqs_q.fasta -r $PWD/gg_13_8_otus/rep_set/97_otus.fasta -o uclust_open_otu</div>
<div data-canvas-width="261.58773669274274"> </div>
<div data-canvas-width="261.58773669274274"><strong>BIOM files</strong></div>
<div data-canvas-width="261.58773669274274"> </div>
<div data-canvas-width="261.58773669274274">
<div data-canvas-width="340.27178909688314">$ biom summarize-table -i uclust_otus/otu_table_even10.biom</div>
<div data-canvas-width="336.3489077155831">$ biom summarize-table -i uclust_otus/otu_table_even10.biom --qualitative</div>
<div data-canvas-width="336.3489077155831"> </div>
<div data-canvas-width="336.3489077155831">
<div data-canvas-width="36.75972696942">$ biom add-metadata -i $PWD/otu_table_even10.biom -o denovo_otu.biom --sample-metadata-fp map_file.txt --observation-metadata-fp $PWD/uclust_assigned_taxonomy/subs_seqs_q_rep_set_tax_assignments.txt --observation-header OTUID,taxonomy --sc-separated taxonomy</div>
<div data-canvas-width="36.75972696942"> </div>
<div data-canvas-width="36.75972696942">
<div data-canvas-width="170.16654266336343">$ biom convert -i otu_table.biom -o otu_table.txt --table-type "otutable" --header-key taxonomy -b</div>
<div data-canvas-width="170.16654266336343"> </div>
<div data-canvas-width="170.16654266336343"><strong>More commands:</strong></div>
<div data-canvas-width="170.16654266336343"> </div>
<div data-canvas-width="170.16654266336343">
<div data-canvas-width="139.10489867925006">$ identify_chimeric_seqs.py -m ChimeraSlayer -i rep_set_aligned.fasta -a gold.fa -o chimeric_seqs.txt</div>
<div data-canvas-width="139.10489867925006"> </div>
<div data-canvas-width="139.10489867925006">
<div data-canvas-width="242.02946585947507">$ core_diversity_analyses.py -i denovo_otu.biom -o core_diversity -e 10 -m map_file.txt -t ref_set.tre</div>
<div data-canvas-width="242.02946585947507"> </div>
<div data-canvas-width="242.02946585947507">
<div data-canvas-width="8.21162356119">1. Filter low sequence count samples from table (minimum sequence count: 7500)</div>
<div data-canvas-width="180.80278075649989">$ filter_samples_from_otu_table.py -i denovo_otu.biom -o core_diversity7500/table_mc7500.biom -n 7500</div>
<div data-canvas-width="8.195135046"> </div>
<div data-canvas-width="8.195135046">2. Rarify the OTU table to 7500 sequences/sample</div>
<div data-canvas-width="211.6897614675269">$ single_rarefaction.py -i core_diversity7500/table_mc7500.biom -o core_diversity7500s/table_even7500.biom -d 7500</div>
<div data-canvas-width="118.20538885050001"> </div>
<div data-canvas-width="118.20538885050001">3. Beta Diversity (weighted_unifrac)</div>
<div data-canvas-width="208.30404989100006">$ beta_diversity.py -i core_diversity7500s/table_even7500.biom -o core_diversity7500/bdiv_even7500/ --metrics weighted_unifrac -t ref_set.tre</div>
<div data-canvas-width="138.79760616749996"> </div>
<div data-canvas-width="138.79760616749996">4. Principal coordinates (weighted_unifrac)</div>
<div data-canvas-width="292.276218062896">$principal_coordinates.py -i core_diversity7500/bdiv_even7500//weighted_unifrac_dm.txt -o core_diversity7500/bdiv_even7500//weighted_unifrac_pc.txt</div>
<div data-canvas-width="135.26950554599995"> </div>
<div data-canvas-width="135.26950554599995">5. Make emperor plots, weighted_unifrac)</div>
<div data-canvas-width="273.1662619582867">$make_emperor.py -i core_diversity7500s/bdiv_even7500//weighted_unifrac_pc.txt -o core_diversity7500/bdiv_even7500//weighted_unifrac_emperor_pcoa_plot/ -m map_file.txt</div>
<div data-canvas-width="65.707899852"> </div>
<div data-canvas-width="65.707899852">6. Alpha rarefaction</div>
<div data-canvas-width="233.74972960500006">$ multiple_rarefactions.py -i core_diversity7500/table_mc7500.biom -m 10 -x 7500 -s 749 -o core_diversity7500/arare_max7500//rarefaction/</div>
<div data-canvas-width="134.085375420381"> </div>
<div data-canvas-width="134.085375420381">7. Alpha diversity on rarefied OTU tables</div>
<div data-canvas-width="220.1165894550002">$ alpha_diversity.py -i core_diversity7500/arare_max7500//rarefaction/ -o core_diversity7500_1105noblanks/arare_max7500//alpha_div/ -t ref_set.tre</div>
<div data-canvas-width="53.216972229456"> </div>
<div data-canvas-width="53.216972229456">8. Collate alpha</div>
<div data-canvas-width="206.24587481400025">$ collate_alpha.py -i core_diversity7500/arare_max7500//alpha_div/ -o core_diversity7500_/arare_max7500//alpha_div_collated/</div>
<div data-canvas-width="99.09537679649996"> </div>
<div data-canvas-width="99.09537679649996">9. Rarefaction plot: All metrics</div>
<div data-canvas-width="217.21417463550023">$ make_rarefaction_plots.py -i core_diversity7500/arare_max7500//</div>
<div data-canvas-width="60.629599911300005">alpha_div_collated/ -m 150701_CAWSMF_1104.txt -o core_diversity7500/arare_max7500//alpha_rarefaction_plots/</div>
<div data-canvas-width="86.586032666007"> </div>
<div data-canvas-width="86.586032666007">10. Summarize Taxonomy</div>
<div data-canvas-width="228.83418719700026">$ summarize_taxa.py -i core_diversity7500s/taxa_plots/table_mc7500_sorted.biom -o core_diversity7500/taxa_plots/</div>
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[STEPS]