#!/bin/bash
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#Andy Rampersaud, 08.07.17
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#Assumptions for this job to run correctly:
#1. You have already run the TopHat_Paired_End 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 "tophat2" folder containing output files
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#Fill in the following information:
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#Need to get the current dir
#SCRIPT_DIR=$(pwd)
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#Need a data set label for output filenames
#Also need data set label to indicate the waxmanlabvm folder
#Dataset_Label="G83"
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#BU Username:
#Need to provide your BU Username so the script knows where to look for UCSC files on the waxmanlabvm
#BU_User="aramp10"
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#Webserver hosting files
#Output files will be hosted on the lab server 
#Log into your account on (waxmanlabvm.bu.edu)
#Make sure the VM_DIR is already created:
#---------------------------------------------------------------------------------
#Webserver location(s) for hosting files
#Note: We are using the waxman-server mount point on the SCC
#VM_DIR_FASTQC=/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/${Dataset_Label}
#VM_DIR_UCSC=/net/waxman-server/mnt/data/waxmanlabvm_home/${BU_User}/${Dataset_Label}
#---------------------------------------------------------------------------------
#In addition to the above dir, you should have your own "Lab_bigBED_Files" dir on the waxmanlabvm
#Feel free to copy my folder if needed
#Remember:
#You'll need to create UCSC track lines for the UCSC Browser to view the data
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#STRAND_RULE option for bam2wig.py:
#---------------------------------------------------------------------------------
#Please use the same option from running the "UCSC_BigWig" job
#This option is used to determine if you have a single bigWig file (STRAND_RULE="none") or if you have a Forward.bw and Reverse.bw file (STRAND_RULE not equal to "none")
#---------------------------------------------------------------------------------
#Choose one:
#Single-end options:
#STRAND_RULE="none"
#STRAND_RULE="+-"
#STRAND_RULE="-+"
#Paired-end options:
#STRAND_RULE="none"
#STRAND_RULE="1++,1--,2+-,2-+"
#STRAND_RULE="1+-,1-+,2++,2--"
#---------------------------------------------------------------------------------
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