#!/bin/bash
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#Andy Rampersaud, 02.08.16
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#Assumptions for this job to run correctly:
#1. You have already run the 04_Bowtie2 job
#2. Your data is organized in the following way:
#You have a data set dir such as:
#/projectnb/wax-es/aramp10/G83_Samples
#Within this dir you have sample specific folders such as:
#G83_M1
#G83_M2
#G83_M3
#G83_M4
#Within each sample specific folder you have a *_R1_*.fastq.gz file and *_R2_*.fastq.gz such as:
#Waxman-TP17_CGATGT_L007_R1_001.fastq.gz
#Waxman-TP17_CGATGT_L007_R2_001.fastq.gz
#Within each sample specific folder you have a "fastq/bowtie2" folder 
#---------------------------------------------------------------------------------
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#Fill in the following information:
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#Information about your data set
#As mentioned above, you should have a data set dir containing your sample specific folders:
#Dataset_DIR="/projectnb/wax-es/aramp10/G83_Samples"
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#Need a data set label for output filenames
#Dataset_Label="G83"
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#Values for heat map color scale:
#---------------------------------------------------------------------------------
#This is useful for seeing the full color spectrum on heat maps
#Using the full color spectrum can highlight certain clusters of samples
#---------------------------------------------------------------------------------
#  --zMin ZMIN, -min ZMIN
#                        Minimum value for the heat map intensities. If not
#                        specified the value is set automatically
#  --zMax ZMAX, -max ZMAX
#                        Maximum value for the heat map intensities.If not
#                        specified the value is set automatically
#---------------------------------------------------------------------------------
#To get these values - you will need to run this job once, look at the heat map, record the min and max correlation values, then re-run this job with those values specified
#If you don't know these values: just use (zMin=0 and zMax=1.0)
#Set values:
#zMin=0.6
#zMax=1.0
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#Please: DO NOT EDIT CODE BELOW
#Additional variables will be populated from if statements
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#Need to get the current dir
#SCRIPT_DIR="$(pwd)"
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#Time hour limit
#On SCC a 12-hour runtime limit is enforced on all jobs, unless specified explicitly. 
#A runtime limit can be specified in the format "hh:mm:ss"
#Dont change the following time limit value unless you know that your job is going to go over 12 hrs 
#TIME_LIMIT="12:00:00"
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