-
Notifications
You must be signed in to change notification settings - Fork 0
/
2016 QIIME Multivariate Script.txt
68 lines (39 loc) · 3.59 KB
/
2016 QIIME Multivariate Script.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
#********************************************************************#
# #
# QIIME v1.9.1 #
# #
# 2016 16S rRNA Multivariate Analysis of 78 Samples #
# #
# Author: Shawn Kroetsch #
# #
#********************************************************************#
## 1) multiple_join_paired_ends.py
## Run join_paired_ends.py on multiple files. Joins paired-end Illumina reads.
multiple_join_paired_ends.py -p /data/shawn/2016_Multivariate/custom_join_param.txt -i /data/shawn/2016_Multivariate/unpaired_input -o /data/shawn/2016_Multivariate/paired_input --read1_indicator '_R1' --read2_indicator '_R2'
## 2) multiple_extract_barcodes.py
## Run extract_barcodes.py on multiple files.
multiple_extract_barcodes.py -p /data/shawn/2016_Multivariate/custom_barcode_param.txt -i /data/shawn/2016_Multivariate/paired_input -o /data/shawn/2016_Multivariate/barcode_output --include_input_dir_path --remove_filepath_in_name
## 3) multiple_split_libraries_fastq.py
## Run split_libraries_fastq.py on multiple files.
multiple_split_libraries_fastq.py -p /data/shawn/2016_Multivariate/custom_quality_param.txt -i /data/shawn/2016_Multivariate/paired_input -o /data/shawn/2016_Multivariate/output --include_input_dir_path --remove_filepath_in_name -m sampleid_by_file
## 4) count_seqs.py
## Count the sequences in a fasta file.
count_seqs.py -i /data/shawn/2016_Multivariate/output/seqs.fna -o /data/shawn/2016_Multivariate/output/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.
pick_de_novo_otus.py -p /data/shawn/2016_Multivariate/custom_de_novo_OTU_param.txt -i /data/shawn/2016_Multivariate/output/seqs.fna -o /data/shawn/2016_Multivariate/de_novo_OTU_output -a -O 20
## 6) parallel_identify_chimeric_seqs.py
## Parallel chimera detection.
parallel_identify_chimeric_seqs.py -i /data/shawn/2016_Multivariate/output/seqs.fna -o /data/shawn/2016_Multivariate/output/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).
filter_otus_from_otu_table.py -i /data/shawn/2016_Multivariate/de_novo_OTU_output/otu_table.biom -o /data/shawn/2016_Multivariate/de_novo_OTU_output/otu_table_non_chimeric.biom -e /data/shawn/2016_Multivariate/output/chimeric_seqs.txt
## 8) filter_otus_from_otu_table.py
## Filter OTUs from an OTU table based on their observation counts or identifier (singleton sequences).
filter_otus_from_otu_table.py -i /data/shawn/2016_Multivariate/de_novo_OTU_output/otu_table_non_chimeric.biom -o /data/shawn/2016_Multivariate/de_novo_OTU_output/de_novo_OTU_table_filtered.biom -n 2
## 9) biom summarize-table
## Takes a BIOM file and prints a summary of the count information on a per-sample basis.
biom summarize-table -i /data/shawn/2016_Multivariate/de_novo_OTU_output/otu_table_non_chimeric.biom -o /data/shawn/2016_Multivariate/de_novo_OTU_output/de_novo_OTU_table_summary.txt
## 10) biom convert
## Convert biom format to tab-delimited table format.
biom convert -i /data/shawn/2016_Multivariate/de_novo_OTU_output/otu_table_non_chimeric.biom -o /data/shawn/2016_Multivariate/de_novo_OTU_output/de_novo_OTU_table_readable_summary.txt --to-tsv