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pairedEndCode.rtf
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pairedEndCode.rtf
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{\rtf1\ansi\ansicpg1252\cocoartf1347\cocoasubrtf570
{\fonttbl\f0\fnil\fcharset0 Menlo-Bold;\f1\fnil\fcharset0 Menlo-Regular;\f2\fmodern\fcharset0 Courier;
\f3\fmodern\fcharset0 Courier-Bold;}
{\colortbl;\red255\green255\blue255;}
\margl1440\margr1440\vieww10800\viewh6980\viewkind0
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural
\f0\b\fs22 \cf0 \CocoaLigature0 Paired End Analysis
\f1\b0 \
\
\f0\b #Joining the forward and reverse reads
\f1\b0 \
join_paired_ends.py -f pairedEndRat/KelleyPool_S1_L001_R1_001.fastq -r pairedEndRat/KelleyPool_S1_L001_R2_001.fastq -o pairedEndSeq\
\
\f0\b #Converting FASTQ file to FASTA(.fna) and QUAL(.qual) file\
\f1\b0 convert_fastaqual_fastq.py -c fastq_to_fastaqual -f pairedEndSeq/fastQ_files/fastqjoin.join.fastq -o pairedEndSeq/fastqConvert/\
\
\f0\b #Splitting and demultiplexing join reads by barcode/sample\
\pard\pardeftab720
\f2\b0\fs24 \cf0 \expnd0\expndtw0\kerning0
\CocoaLigature1 split_libraries.py -m QIIME_data/Update_Rat_Map.txt -f pairedEndSeq/fastqConvert/fastqjoin.join.fna -q pairedEndSeq/fastqConvert/fastqjoin.join.qual -o pairedEndSeq/01_splitLibraries\
\
\f3\b #Pick de novo OTUs and assigning taxonomy\
\f2\b0 pick_de_novo_otus.py -i pairedEndSeq/01_splitLibraries/seqs.fna -o pairedEndSeq/02_OTUs\
\
\f3\b Filtering biom tables (Found in 02_OTUS/biom_tables)
\f2\b0 \
\f3\b \
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural
\f0\fs22 \cf0 \kerning1\expnd0\expndtw0 \CocoaLigature0 #1. Filtered OTUs present in less than 25% (22) of the samples in table\
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural
\f1\b0 \cf0 filter_otus_from_otu_table.py -i pairedEndSeq/02_OTUs/biom_tables/ otu_table.biom -o pairedEndSeq/02_OTUs/biom_tables/Min22_table -s 22\
\
\f0\b #2. Filtered sequences found in samples at time 0 (for alpha and beta diversity and kruskal-wallis)\
\f1\b0 filter_samples_from_otu_table.py -i pairedEndSeq/02_OTUs/biom_tables/ Min22_table.biom -o pairedEndSeq/02_OTUs/biom_tables/noTime0.biom -m QIIME_data/Update_Rat_Map.txt -s 'Date:*,!3_30_14'\
\
#3.
\f0\b Filter sequences that are only found in the control group (non-drinkers)\
\f1\b0 filter_samples_from_otu_table.py -i pairedEndSeq/02_OTUs/biom_tables/ Min22_table.biom -o pairedEndSeq/02_OTUs/biom_tables/nonDrinkers.biom -m QIIME_data/Update_Rat_Map.txt -s 'Description:1'\
\
#4.
\f0\b Filter sequences that are from Time 0 found in the control group (non- drinkers)\
\f1\b0 filter_samples_from_otu_table.py -i pairedEndSeq/02_OTUs/biom_tables/ nonDrinkers.biom -o pairedEndSeq/02_OTUs/biom_tables/nonDrinkers_noT0.biom -m QIIME_data/Update_Rat_Map.txt -s 'Date:*,!3_30_14'\
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural
\f0\b \cf0 \
\f1\b0 #5.
\f0\b Filter sequences that are only found in the treatment group (drinkers)\
\f1\b0 filter_samples_from_otu_table.py -i pairedEndSeq/02_OTUs/biom_tables/ Min22_table.biom -o pairedEndSeq/02_OTUs/biom_tables/drinkers.biom -m QIIME_data/Update_Rat_Map.txt -s 'Description:2'\
\
\f0\b #6.Filter sequences that are from Time 0 found in the treatment group (drinkers) \
\f1\b0 filter_samples_from_otu_table.py -i pairedEndSeq/02_OTUs/biom_tables/ drinkers.biom -o pairedEndSeq/02_OTUs/biom_tables/drinkers_noT0.biom -m QIIME_data/Update_Rat_Map.txt -s 'Date:*,!3_30_14'\
\f0\b \
#Alpha Diversity (Shannon, Chao, PD, observed_species)\
#NO TIME ZERO\
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural
\f1\b0 \cf0 alpha_rarefaction.py -i pairedEndSeq/02_OTUs/biom_tables/noTime0.biom -m QIIME_data/Update_Rat_Map.txt -o pairedEndSeq/03_alphaDiv/ -p QIIME_data/ 10_alpha_div/alpha_params.txt -t pairedEndSeq/02_OTUs/rep_set.tre \
\
\f0\b #Creating table with alpha measures for R\
\f1\b0 alpha_diversity.py -i pairedEndSeq/02_OTUs/biom_tables/noTime0.biom -m shannon,PD_whole_tree,observed_species,chao1 -o pairedEndSeq/03_alphaDiv/ alphaMeasures.txt -t pairedEndSeq/02_OTUs/rep_set.tre\
\
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural
\f0\b \cf0 #Beta Diversity (NO TIME ZERO)\
#Control vs. Treatmnet\
\f1\b0 beta_diversity_through_plots.py -i pairedEndSeq/02_OTUs/biom_tables/ noTime0.biom -m QIIME_data/Update_Rat_Map.txt -o pairedEndSeq/04_betaDiv/ beta_controlVStreat/ -t pairedEndSeq/02_OTUs/rep_set.tre -e 4865
\f0\b \
\
#Control Group (Time points)\
\f1\b0 beta_diversity_through_plots.py -i pairedEndSeq/02_OTUs/biom_tables/ nonDrinkers_noT0.biom -m QIIME_data/Update_Rat_Map.txt -o pairedEndSeq/ 04_betaDiv/Control_time -t pairedEndSeq/02_OTUs/rep_set.tre -e 4865\
\
#
\f0\b Treatment Group (Time points)\
\f1\b0 beta_diversity_through_plots.py -i pairedEndSeq/02_OTUs/biom_tables/ drinkers_noT0.biom -m QIIME_data/Update_Rat_Map.txt -o pairedEndSeq/ 04_betaDiv/ Treatment_time -t pairedEndSeq/02_OTUs/rep_set.tre -e 4865\
\
\f0\b #ANOSIM analysis\
#Non-drinkers vs. drinkers without Time 0\
\f1\b0 #Unweighted:\
compare_categories.py --method anosim -i pairedEndSeq/04_betaDiv/ beta_controlVStreat/unweighted_unifrac_dm.txt -m QIIME_data/ Update_Rat_Map.txt -c Description -o pairedEndSeq/04_betaDiv/ beta_controlVStreat/anosim_unweighted\
\
#Weighted:\
compare_categories.py --method anosim -i pairedEndSeq/04_betaDiv/ beta_controlVStreat/weighted_unifrac_dm.txt -m QIIME_data/ Update_Rat_Map.txt -c Description -o pairedEndSeq/04_betaDiv/ beta_controlVStreat/anosim_weighted\
\
\f0\b #Non-drinkers over time (T1-T3)\
\f1\b0 #Unweighted:\
compare_categories.py --method anosim -i pairedEndSeq/04_betaDiv/ Control_time/unweighted_unifrac_dm.txt -m QIIME_data/Update_Rat_Map.txt - c Time_point -o pairedEndSeq/04_betaDiv/Control_time/anosim_unweighted\
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural
\cf0 \
#Weighted:\
compare_categories.py --method anosim -i pairedEndSeq/04_betaDiv/ Control_time/weighted_unifrac_dm.txt -m QIIME_data/Update_Rat_Map.txt -c Time_point -o pairedEndSeq/04_betaDiv/Control_time/anosim_weighted\
\
\f0\b Drinkers over time (T1-T3)\
\f1\b0 #Unweighted:\
compare_categories.py --method anosim -i pairedEndSeq/04_betaDiv/ Treatment_time/unweighted_unifrac_dm.txt -m QIIME_data/Update_Rat_Map.txt -c Time_point -o pairedEndSeq/04_betaDiv/Treatment_time/anosim_unweighted\
\
#Weighted:\
compare_categories.py --method anosim -i pairedEndSeq/04_betaDiv/ Treatment_time/weighted_unifrac_dm.txt -m QIIME_data/Update_Rat_Map.txt - c Time_point -o pairedEndSeq/04_betaDiv/Treatment_time/anosim_weighted\
\
\
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural
\f0\b \cf0 #Kruskal-Wallis Group Significance\
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural
\f1\b0 \cf0
\f0\b # Non-drinkers vs. drinkers without Time 0\
\f1\b0 group_significance.py -i pairedEndSeq/02_OTUs/biom_tables/noTime0.biom -m QIIME_data/Update_Rat_Map.txt -c Description -s kruskal_wallis -o pairedEndSeq/05_groupSig/kruskal_controlVStreat.txt \'97- biom_samples_are_superset\
\
\f0\b #Across time points (1-3) in the drinkers\
\f1\b0 group_significance.py -i pairedEndSeq/02_OTUs/biom_tables/drinkers_noT0.biom -m QIIME_data/Update_Rat_Map.txt -c Time_point -s kruskal_wallis -o pairedEndSeq/05_groupSig/kruskal_drinkers.txt --biom_samples_are_superset\
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural
\f0\b \cf0 \
#Across time points (1-3) in the non-drinkers\
\f1\b0 group_significance.py -i pairedEndSeq/02_OTUs/biom_tables/ nonDrinkers_noT0.biom -m QIIME_data/Update_Rat_Map.txt -c Time_point -s kruskal_wallis -o pairedEndSeq/05_groupSig/kruskal_nonDrinkers.txt -- biom_samples_are_superset\
\
#
\f0\b Significant Unassigned Sequences\
\f1\b0 >denovo3843 CC02B_41014\
CCTGTTCGATACCCGCGCTTTCGAGCTTCAGCGTCAGTTGCGCCCCAGTGAGCTGCCTTCGCAATCGGAGTTCTTCGTGATATCTAAGCATTTCACCGCTACACCACGAATTCCGCCCACTTTATGCGTACTCAAGGAAACCAGTTCGCGCTGCAGTGCAGATGTTGAGCATCTTCATTTCACAACACGCTTCATCTCCGGCCTCCGCTCCCTTTTAACCCAATACATCCGGATACCTCCGCGACCTTCCGTATTAACCCGTACGCTGCCCGTCGTGGTGTGTATGAAATCCGTTGCGACGCCCGCGCTTTAGCGCTTCAGCGTCAGGTGCGCCTGAGTGAGCTGCCTTCGAAATCTGAGTTCGTCGTGATATCTAAGCATTTCACCGCTACACCACGAATTCCGCCCACTCTATGCGTACTCAAGGAAACCAGTTCGCGCTGCAGTGCAGATGTTGAGCATCTACATTTCACAACACGCTTAATCTCCGGCCTACGCTCCCTTTAAACCCAATAAATCCGGATAACGCCCGGACCTTCCGTATTACCGCGGCGGCTGGCAC\
\
>denovo7064 CC24D_3534\
CCTGTTCGATACCCGCGCTTTCGAGCTTCAGCGTCAGTTGCGCCCCAGTGAGCTGCCTTCGCAATCGGAGTTCTTCGTGATATCTAAGCATTTCACCGCTACACCACGAATTCCGCCCACTTTATGCGTACTCAAGGAAACCAGTTCGCGCTGCAGTGCAGATGTTGAGCATCTACATTTCACAACACGCTTAATCTCCGGCATACGCTCCCTTTAAAACCAATAAATCCGCATAACGCCCGGCCCCTCCGTATTACAGCGGGCGCCCCACTACTACCGGGTTTTTTACCCCGGTTCGCCGCCCCCGCTGTCGAGCTTAAGCGCCGTTTGCGCCCCAGTGAGCTGTCTTCGTAAGCGGAGTTCTTCGTGATATCTAAGCATTTCACCGCTACACCACGAATTCCGCCCACTTTATGCGTACTCAAGGAAACCAGTTCGCGCTGAAGTGCAGATGTTGAGCATCTACATTTCACAACACGCTTAATCTCCGGCCTACGCTCCCTTTAAACCCAATAAATCCGGATAACGCCCGGACCCTCCGTATTACCGCGGCGGCTGGCAC\
\
>denovo9845 CC11A_1205378\
CCTGTTCGATACCCGCACTTTCGAGCCTCAATGTCTGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTCTTCGTGATATCTAAGCATTTCACCGCTACACCACGAATTCCGCCTGCCTCACCTGCACTCAAGACATCCAGTATCAACTGCAATTTTACGGTTGAGCCGCAAACTTTCACAACTGACTTAAACATCCATCTACGCTCCCTTTAAACCCAATAAATCCGGATAACGCTCGGATCCTCCGTATTACCGCGGATGCCTCCGTGCGACAAGGGTTTCTAATCCTGTTCGTTCCCCGAACTTTGCGGCCTCAATGTCTGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTCTTCTTGATATCTAAGCATTTCACCGCTACACCACGAATTCCGCCTGCCTCAACTGCACTCAAGACATCCAGTATCAACTGCAATTTTACGGTTGAGCCGCAAACTTTCACAACTGACTTAAACATCCATCTACGCTCCCTGTAAACCCAATAACTCCGGATAACGCTCGGATCCTCCGTATTACCGCGGCTGCTGGCAN\
\
\f0\b #Converting biom table to text file\
\f1\b0 biom convert -i pairedEndSeq/02_OTUs/biom_tables/noTime0.biom -o pairedEndSeq/02_OTUs_biom_tables/noTime0.txt --to-tsv}