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#*********************************************************************#
# #
# QIIME v1.9.1 #
# #
# 16S rRNA Univariate Analysis of 2016 vs 2017 Samples #
# #
# Author: Shawn Kroetsch #
# #
#*********************************************************************#
## 1) multiple_join_paired_ends.py
## Run join_paired_ends.py on multiple files. Joins paired-end Illumina reads.
# Sampling Year:
multiple_join_paired_ends.py -p /data/shawn/2016_&_2017_Univariate/custom_join_param.txt -i /data/shawn/2016_&_2017_Univariate/unpaired_input_sampling_year_physella -o /data/shawn/2016_&_2017_Univariate/paired_input_sampling_year_physella --read1_indicator '_R1' --read2_indicator '_R2'
multiple_join_paired_ends.py -p /data/shawn/2016_&_2017_Univariate/custom_join_param.txt -i /data/shawn/2016_&_2017_Univariate/unpaired_input_sampling_year_ephemeroptera -o /data/shawn/2016_&_2017_Univariate/paired_input_sampling_year_ephemeroptera --read1_indicator '_R1' --read2_indicator '_R2'
## 2) multiple_extract_barcodes.py
## Run extract_barcodes.py on multiple files.
# Sampling Year:
multiple_extract_barcodes.py -p /data/shawn/2016_&_2017_Univariate/custom_barcode_param.txt -i /data/shawn/2016_&_2017_Univariate/paired_input_sampling_year_physella -o /data/shawn/2016_&_2017_Univariate/barcode_output_sampling_year_physella --include_input_dir_path --remove_filepath_in_name
multiple_extract_barcodes.py -p /data/shawn/2016_&_2017_Univariate/custom_barcode_param.txt -i /data/shawn/2016_&_2017_Univariate/paired_input_sampling_year_ephemeroptera -o /data/shawn/2016_&_2017_Univariate/barcode_output_sampling_year_ephemeroptera --include_input_dir_path --remove_filepath_in_name
## 3) multiple_split_libraries_fastq.py
## Run split_libraries_fastq.py on multiple files.
# Sampling Year:
multiple_split_libraries_fastq.py -p /data/shawn/2016_&_2017_Univariate/custom_quality_param.txt -i /data/shawn/2016_&_2017_Univariate/paired_input_sampling_year_physella -o /data/shawn/2016_&_2017_Univariate/output_sampling_year_physella --include_input_dir_path --remove_filepath_in_name -m sampleid_by_file
multiple_split_libraries_fastq.py -p /data/shawn/2016_&_2017_Univariate/custom_quality_param.txt -i /data/shawn/2016_&_2017_Univariate/paired_input_sampling_year_ephemeroptera -o /data/shawn/2016_&_2017_Univariate/output_sampling_year_ephemeroptera --include_input_dir_path --remove_filepath_in_name -m sampleid_by_file
## 4) count_seqs.py
## Count the sequences in a fasta file.
# Sampling Year:
count_seqs.py -i /data/shawn/2016_&_2017_Univariate/output_sampling_year_physella/seqs.fna -o /data/shawn/2016_&_2017_Univariate/output_sampling_year_physella/seqs_count.txt
count_seqs.py -i /data/shawn/2016_&_2017_Univariate/output_sampling_year_ephemeroptera/seqs.fna -o /data/shawn/2016_&_2017_Univariate/output_sampling_year_ephemeroptera/seqs_count.txt
## 5) pick_de_novo_otus.py
## A workflow for de novo OTU picking, taxonomy assignment, phylogenetic tree construction, and OTU table construction.
# Sampling Year:
pick_de_novo_otus.py -p /data/shawn/2016_&_2017_Univariate/custom_de_novo_OTU_param.txt -i /data/shawn/2016_&_2017_Univariate/output_sampling_year_physella/seqs.fna -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella -a -O 20
pick_de_novo_otus.py -p /data/shawn/2016_&_2017_Univariate/custom_de_novo_OTU_param.txt -i /data/shawn/2016_&_2017_Univariate/output_sampling_year_ephemeroptera/seqs.fna -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera -a -O 20
## 6) parallel_identify_chimeric_seqs.py
## Parallel chimera detection.
# Sampling Year:
parallel_identify_chimeric_seqs.py -i /data/shawn/2016_&_2017_Univariate/output_sampling_year_physella/seqs.fna -o /data/shawn/2016_&_2017_Univariate/output_sampling_year_physella/chimeric_seqs.txt -O 20
parallel_identify_chimeric_seqs.py -i /data/shawn/2016_&_2017_Univariate/output_sampling_year_ephemeroptera/seqs.fna -o /data/shawn/2016_&_2017_Univariate/output_sampling_year_ephemeroptera/chimeric_seqs.txt -O 20
## 7) filter_otus_from_otu_table.py
## Filter OTUs from an OTU table based on their observation counts or identifier (chimeric sequences).
# Sampling Year:
filter_otus_from_otu_table.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/otu_table.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/otu_table_non_chimeric.biom -e /data/shawn/2016_&_2017_Univariate/output_sampling_year_physella/chimeric_seqs.txt
filter_otus_from_otu_table.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/otu_table.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/otu_table_non_chimeric.biom -e /data/shawn/2016_&_2017_Univariate/output_sampling_year_ephemeroptera/chimeric_seqs.txt
## 8a) filter_otus_from_otu_table.py
## Filter OTUs from an OTU table based on their observation counts or identifier (singleton sequences).
# Sampling Year:
filter_otus_from_otu_table.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/otu_table_non_chimeric.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_filtered.biom -n 2
filter_otus_from_otu_table.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/otu_table_non_chimeric.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_filtered.biom -n 2
## 8b) filter_otus_from_otu_table.py
## Filter OTUs from an OTU table based on their observation counts or identifier (singleton sequences; using rare OTU table).
# Sampling Year:
filter_otus_from_otu_table.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/otu_table_non_chimeric.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_filtered_rare.biom -s 5
filter_otus_from_otu_table.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/otu_table_non_chimeric.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_filtered_rare.biom -s 5
## 9a) biom summarize-table
## Takes a BIOM file and prints a summary of the count information on a per-sample basis.
# Sampling Year:
biom summarize-table -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/otu_table_non_chimeric.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_summary.txt
biom summarize-table -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/otu_table_non_chimeric.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_summary.txt
## 9b) biom summarize-table
## Takes a BIOM file and prints a summary of the count information on a per-sample basis (using rare OTU table).
# Sampling Year:
biom summarize-table -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_filtered_rare.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_summary_rare.txt
biom summarize-table -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_filtered_rare.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_summary_rare.txt
## 10a) biom convert
## Convert biom format to tab-delimited table format.
# Sampling Year:
biom convert -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_filtered.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_readable_summary.txt --to-tsv
biom convert -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_filtered.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_readable_summary.txt --to-tsv
## 10b) biom convert
## Convert biom format to tab-delimited table format (using rare OTU table).
# Sampling Year:
biom convert -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_filtered_rare.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_readable_summary_rare.txt --to-tsv
biom convert -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_filtered_rare.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_readable_summary_rare.txt --to-tsv
## 11) validate_mapping_file.py
## Checks user’s metadata mapping file for required data, valid format.
# Sampling Year:
validate_mapping_file.py -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -o /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella -v
validate_mapping_file.py -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -o /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera -v
## 12a) alpha_rarefaction.py
## A workflow script for performing alpha rarefaction.
# Sampling Year:
alpha_rarefaction.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_filtered.biom -o /data/shawn/2016_&_2017_Univariate/alpha_diversity_output_sampling_year_physella -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -e 10000 -t /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/rep_set.tre -a -O 20 -p /data/shawn/2016_&_2017_Univariate/custom_alpha_diversity_param.txt
alpha_rarefaction.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_filtered.biom -o /data/shawn/2016_&_2017_Univariate/alpha_diversity_output_sampling_year_ephemeroptera -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -e 10000 -t /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/rep_set.tre -a -O 20 -p /data/shawn/2016_&_2017_Univariate/custom_alpha_diversity_param.txt
## 12b) alpha_rarefaction.py
## A workflow script for performing alpha rarefaction (using rare OTU table).
# Sampling Year:
alpha_rarefaction.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_filtered_rare.biom -o /data/shawn/2016_&_2017_Univariate/alpha_diversity_output_sampling_year_physella_rare -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -e 10000 -t /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/rep_set.tre -a -O 20 -p /data/shawn/2016_&_2017_Univariate/custom_alpha_diversity_param.txt
alpha_rarefaction.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_filtered_rare.biom -o /data/shawn/2016_&_2017_Univariate/alpha_diversity_output_sampling_year_ephemeroptera_rare -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -e 10000 -t /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/rep_set.tre -a -O 20 -p /data/shawn/2016_&_2017_Univariate/custom_alpha_diversity_param.txt
## 13a) beta_diversity_through_plots.py
## A workflow script for computing beta diversity distance matrices and generating PCoA plots.
# Sampling Year:
beta_diversity_through_plots.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_filtered.biom -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella -t /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/rep_set.tre -a -e 10000 -O 20 -p /data/shawn/2016_&_2017_Univariate/custom_beta_diversity_param.txt
beta_diversity_through_plots.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_filtered.biom -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera -t /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/rep_set.tre -a -e 10000 -O 20 -p /data/shawn/2016_&_2017_Univariate/custom_beta_diversity_param.txt
## 13b) beta_diversity_through_plots.py
## A workflow script for computing beta diversity distance matrices and generating PCoA plots (using rare OTU table).
# Sampling Year:
beta_diversity_through_plots.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_filtered_rare.biom -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella_rare -t /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/rep_set.tre -a -e 10000 -O 20 -p /data/shawn/2016_&_2017_Univariate/custom_beta_diversity_param.txt
beta_diversity_through_plots.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_filtered_rare.biom -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera_rare -t /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/rep_set.tre -a -e 10000 -O 20 -p /data/shawn/2016_&_2017_Univariate/custom_beta_diversity_param.txt
## 14a) group_significance.py
## Compare OTU frequencies across sample groups (relative abundance with Benjamini-Hochberg corrections).
# Sampling Year:
group_significance.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_filtered.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/group_significance.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -c SamplingYear -s kruskal_wallis
group_significance.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_filtered.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/group_significance.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -c SamplingYear -s kruskal_wallis
## 14b) group_significance.py
## Compare OTU frequencies across sample groups (relative abundance with Benjamini-Hochberg corrections; using rare OTU table).
# Sampling Year:
group_significance.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_filtered_rare.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/group_significance_rare.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -c SamplingYear -s kruskal_wallis
group_significance.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_filtered_rare.biom -o /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/group_significance_rare.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -c SamplingYear -s kruskal_wallis
## 15a) compare_categories.py
## Analyzes statistical significance of sample groupings using distance matrices (unweighted UniFrac).
# Sampling Year:
compare_categories.py --method adonis -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella/unweighted_unifrac_dm.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -c SamplingYear -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella/adonis/unweighted_unifrac/adonis_unweighted_unifrac_sampling_year
compare_categories.py --method adonis -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera/unweighted_unifrac_dm.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -c SamplingYear -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera/adonis/unweighted_unifrac/adonis_unweighted_unifrac_sampling_year
## 15b) compare_categories.py
## Analyzes statistical significance of sample groupings using distance matrices (unweighted UniFrac; using rare OTU table).
# Sampling Year:
compare_categories.py --method adonis -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella_rare/unweighted_unifrac_dm.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -c SamplingYear -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella_rare/adonis/unweighted_unifrac/adonis_unweighted_unifrac_sampling_year
compare_categories.py --method adonis -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera_rare/unweighted_unifrac_dm.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -c SamplingYear -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera_rare/adonis/unweighted_unifrac/adonis_unweighted_unifrac_sampling_year
## 16a) compare_categories.py
## Analyzes statistical significance of sample groupings using distance matrices (weighted UniFrac).
# Sampling Year:
compare_categories.py --method adonis -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella/weighted_unifrac_dm.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -c SamplingYear -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella/adonis/weighted_unifrac/adonis_weighted_unifrac_sampling_year
compare_categories.py --method adonis -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera/weighted_unifrac_dm.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -c SamplingYear -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera/adonis/weighted_unifrac/adonis_weighted_unifrac_sampling_year
## 16b) compare_categories.py
## Analyzes statistical significance of sample groupings using distance matrices (weighted UniFrac; using rare OTU table).
# Sampling Year:
compare_categories.py --method adonis -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella_rare/weighted_unifrac_dm.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -c SamplingYear -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella_rare/adonis/weighted_unifrac/adonis_weighted_unifrac_sampling_year
compare_categories.py --method adonis -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera_rare/weighted_unifrac_dm.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -c SamplingYear -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera_rare/adonis/weighted_unifrac/adonis_weighted_unifrac_sampling_year
## 17a) compare_categories.py
## Analyzes statistical significance of sample groupings using distance matrices (Bray-Curtis).
# Sampling Year:
compare_categories.py --method adonis -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella/bray_curtis_dm.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -c SamplingYear -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella/adonis/bray_curtis/adonis_bray_curtis_sampling_year
compare_categories.py --method adonis -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera/bray_curtis_dm.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -c SamplingYear -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera/adonis/bray_curtis/adonis_bray_curtis_sampling_year
## 17b) compare_categories.py
## Analyzes statistical significance of sample groupings using distance matrices (Bray-Curtis; using rare OTU table).
# Sampling Year:
compare_categories.py --method adonis -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella_rare/bray_curtis_dm.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -c SamplingYear -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella_rare/adonis/bray_curtis/adonis_bray_curtis_sampling_year
compare_categories.py --method adonis -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera_rare/bray_curtis_dm.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -c SamplingYear -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera_rare/adonis/bray_curtis/adonis_bray_curtis_sampling_year
## 18a) make_2d_plots.py
## Make 2D PCoA Plots (unweighted UniFrac).
# Sampling Year:
make_2d_plots.py -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella/unweighted_unifrac_pc.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella/2d_unweighted_unifrac_plots -b SamplingYear
make_2d_plots.py -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera/unweighted_unifrac_pc.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera/2d_unweighted_unifrac_plots -b SamplingYear
## 18b) make_2d_plots.py
## Make 2D PCoA Plots (unweighted UniFrac; using rare OTU table).
# Sampling Year:
make_2d_plots.py -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella_rare/unweighted_unifrac_pc.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella_rare/2d_unweighted_unifrac_plots -b SamplingYear
make_2d_plots.py -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera_rare/unweighted_unifrac_pc.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera_rare/2d_unweighted_unifrac_plots -b SamplingYear
## 19a) make_2d_plots.py
## Make 2D PCoA Plots (weighted UniFrac).
# Sampling Year:
make_2d_plots.py -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella/weighted_unifrac_pc.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella/2d_weighted_unifrac_plots -b SamplingYear
make_2d_plots.py -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera/weighted_unifrac_pc.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera/2d_weighted_unifrac_plots -b SamplingYear
## 19b) make_2d_plots.py
## Make 2D PCoA Plots (weighted UniFrac; using rare OTU table).
# Sampling Year:
make_2d_plots.py -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella_rare/weighted_unifrac_pc.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella_rare/2d_weighted_unifrac_plots -b SamplingYear
make_2d_plots.py -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera_rare/weighted_unifrac_pc.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera_rare/2d_weighted_unifrac_plots -b SamplingYear
## 20a) make_2d_plots.py
## Make 2D PCoA Plots (Bray-Curtis).
# Sampling Year:
make_2d_plots.py -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella/bray_curtis_pc.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella/2d_bray_curtis_plots -b SamplingYear
make_2d_plots.py -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera/bray_curtis_pc.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera/2d_bray_curtis_plots -b SamplingYear
## 20b) make_2d_plots.py
## Make 2D PCoA Plots (Bray-Curtis; using rare OTU table).
# Sampling Year:
make_2d_plots.py -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella_rare/bray_curtis_pc.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_physella_rare/2d_bray_curtis_plots -b SamplingYear
make_2d_plots.py -i /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera_rare/bray_curtis_pc.txt -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -o /data/shawn/2016_&_2017_Univariate/beta_diversity_output_sampling_year_ephemeroptera_rare/2d_bray_curtis_plots -b SamplingYear
## 21a) summarize_taxa_through_plots.py
## A workflow script for performing taxonomy summaries and plots.
# Sampling Year:
summarize_taxa_through_plots.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella/de_novo_OTU_table_filtered.biom -o /data/shawn/2016_&_2017_Univariate/summarize_taxa_through_plots_output_sampling_year_physella -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -p /data/shawn/2016_&_2017_Univariate/custom_summary_through_plots_param.txt
summarize_taxa_through_plots.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera/de_novo_OTU_table_filtered.biom -o /data/shawn/2016_&_2017_Univariate/summarize_taxa_through_plots_output_sampling_year_ephemeroptera -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -p /data/shawn/2016_&_2017_Univariate/custom_summary_through_plots_param.txt
## 21b) summarize_taxa_through_plots.py
## A workflow script for performing taxonomy summaries and plots (using rare OTU table).
# Sampling Year:
summarize_taxa_through_plots.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_physella_rare/de_novo_OTU_table_filtered.biom -o /data/shawn/2016_&_2017_Univariate/summarize_taxa_through_plots_output_sampling_year_physella_rare -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_physella/mapping_file_2016_2017_sampling_year_physella.txt -p /data/shawn/2016_&_2017_Univariate/custom_summary_through_plots_param.txt
summarize_taxa_through_plots.py -i /data/shawn/2016_&_2017_Univariate/de_novo_OTU_output_sampling_year_ephemeroptera_rare/de_novo_OTU_table_filtered.biom -o /data/shawn/2016_&_2017_Univariate/summarize_taxa_through_plots_output_sampling_year_ephemeroptera_rare -m /data/shawn/2016_&_2017_Univariate/mapping_file_output_2016_2017_sampling_year_ephemeroptera/mapping_file_2016_2017_sampling_year_ephemeroptera.txt -p /data/shawn/2016_&_2017_Univariate/custom_summary_through_plots_param.txt