#!/bin/bash
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#Andy Rampersaud, 01.27.16
#Adapted from diff_exp scripts by Tisha Melia
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#Assumptions for this job to run correctly:
#1. You have already run the TopHat_Paired_End job
#2. You have already run the Extract_Counts_* job(s)
#3. 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 "fastq" folder with:
#Files: *_R1_*.fastq.gz 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 "tophat2" folder containing output files
#Within each "tophat2" folder you have a "HTSeq" folder containing output files
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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"
#---------------------------------------------------------------------------------
#Need a data set label for SEGEX output filenames
#Dataset_Label="G83"
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#GTF_Files_DIR
#Need this dir that contains the various GTF files
#Feel free to use my dir but it's better practice to have a copy in your own Dataset_DIR
#GTF_Files_DIR="/projectnb/wax-es/aramp10/GTF_Files"
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#Information about the conditions being compared
#The differential expression will output the fold change in the following
#format: CONDITION_2/CONDITION_1
#--------------------------------------------------------------------------------
#Note about CONDITION_*_NAME:
#Do not use *spaces* for CONDITION_*_NAME (this will prevent the job from running correctly)
#Please use underscores in place of spaces
#--------------------------------------------------------------------------------
#CONDITION_1_NAME="Female"
#CONDITION_2_NAME="Male"
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#Comparison Number
#If you are doing multiple comparisons within the same dataset, it's helpful to number each comparison
#For example:
#Comparison: STAT5_High_VS_STAT5_Low, Output Folders: Output_DiffExp_1a, Output_DiffExp_1b, Output_DiffExp_1c
#Comparison: Hypox_30min_VS_Hypox_male, Output Folders: Output_DiffExp_2a, Output_DiffExp_2b, Output_DiffExp_2c
#Comparison: Hypox_90min_VS_Hypox_male, Output Folders: Output_DiffExp_3a, Output_DiffExp_3b, Output_DiffExp_3c
#COMPAR_NUM=1
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#Please: DO NOT EDIT CODE BELOW
#Additional variables will be populated from if statements
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#Couting program used
#Note that the DiffExp.qsub scripts are custom for the counting program used
#No options for this variable (constant value)
#COUNT_PROGRAM="featureCounts"
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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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