wilkox

#!/bin/bash
#
#PBS -l nodes=1:ppn=16
#PBS -j oe
#PBS -k oe

date

#Set base dir and SparCC path
if [ `hostname` == "Davids-MacBook-Air.local" ]; then

wilkox

#Prepare output directories
system("rm -rf OTU_tables")
system("mkdir OTU_tables")

#Load OTU table
OTUTable <- read.tidy.dt("../picked_OTUs_winter_forward/final_otu_table_mc2.clean.tidy.txt")

#Load sample metadata
Samples <- read.tidy("../samples/samples.txt")

wilkox

#!/usr/bin/perl

use Modern::Perl 2014;
use autodie;
use Getopt::Long;
use File::Slurp qw(read_file);
$|++;

my $USAGE = q/USAGE:
perl select_OTUs_and_samples.pl -m <map file> -o <list of OTUs> -s <list of samples> -f <reads fasta file> -u <output fasta file>

wilkox

#Load OTU table
OTUTable <- read.tidy("../picked_OTUs_forward/final_otu_table_mc2_w_taxonomy.clean.tidy.txt")

#Add sample data
Samples <- read.tidy("../samples/samples.txt")
OTUTable <- merge(OTUTable, Samples[c("Sample", "Location", "Type")], by = "Sample", all.x = TRUE)

#Select skin/surface samples
OTUTable <- OTUTable[which(OTUTable$Type %in% c("Skin", "Surface")), ]

wilkox

#Libraries
library(wilkoxmisc)

#Global variables
OTUTablePath <- "PUT-PATH-HERE" #This is the OTU table with taxonomy
ContaminantOTUPath <- "PUT-PATH-HERE" #This is the list of contaminant OTUs
PlotPath <- "PUT-PATH-HERE" #This is where the plot will be written, should end in .pdf
BlankSamples <- c("Blk", "Blk2") #These are the blank samples

#Read in OTU table

wilkox

#Libraries
library(wilkoxmisc)

#Global variables
OTUTablePath <- "PUT-PATH-HERE" #This is the OTU table with taxonomy
ContaminantOTUPath <- "PUT-PATH-HERE" #This is where the list of contaminant OTUs will be written
ContaminantLineagePath <- "PUT-PATH-HERE" #This is where the list of contaminant lineages will be written
BlankSamples <- c("Blk", "Blk2") #These are the blank samples
CutoffValue <- 0.01 #This is the threshold relative abundance for a lineage to be a contaminant

wilkox

Sample	Digester	Substrate	Year	Replicate
GZ-cell-35-1	GZ	Cellulose	2	1
GZ-cell-35-2	GZ	Cellulose	2	2
GZ-cell-35-3	GZ	Cellulose	2	3
GZ-cell-35-4	GZ	Cellulose	2	4
GZ-cell-35-gDNA	GZ	Cellulose	1	
GZ-xylan-35-1	GZ	Xylan	2	1
GZ-xylan-35-2	GZ	Xylan	2	2
GZ-xylan-35-3	GZ	Xylan	2	3
GZ-xylan-35-4	GZ	Xylan	2	4

wilkox

#SampleID	BarcodeSequence	LinkerPrimerSequence
ADMa2BHBSPR		
ADMa2SWCWINT		
ADMa2RMCWINT		
ADMa2BHBWINT		
ADMa2TFBWINT		
ADMa3ZLPWIN		
ADMa2TFBSPR		
ADMa2BLKWINT		
ADMa2SWCSPR		

wilkox

#!/bin/bash
#
#PBS -l nodes=compute-1-19:ppn=16
#PBS -j oe
#PBS -k oe

date

#Set base directory
if [ `hostname` == "Davids-MacBook-Air.local" ]; then

wilkox

#!/bin/bash
#
#PBS -l nodes=1:ppn=16
#PBS -j oe
#PBS -k oe

date

#Set base dir
if [ `hostname` == "Davids-MacBook-Air.local" ]; then