We run FastQC using a script called run_fastqc. The first part of the script (/campusdata/ndudek/FastQC/fastqc), specifies the location of the fastqc program to be run. The second part (/campusdata/rcalef/remove_dup/SW018_adapterTrimmed_dupRemoved_150424_R1.fastq/), the library to be used which in this example (SW018_adapterTrimmed_dupRemoved_150424_R1.fastq/) was a HiSeq 2 X 100 library. The script here uses four libraries as input. This is why we have the same command repeated four times for the different libraries. The third part (-o /campusdata/gchaves/fastqc_trimmed_PCR_duplicates/), specifies where to locate the output. The type of unix shell used was bash. Here is the run_fastqc script:

#!/bin/bash # #$ -cwd #$ -j y #$ -S /bin/bash #

date

PATH=“/usr/java/jdk1.7.0_03/bin/:${PATH}” export PATH

/campusdata/ndudek/FastQC/fastqc /campusdata/rcalef/remove_dup/SW018_adapterTrimmed_dupRemoved_150424_R1.fastq/ -o /campusdata/gchaves/fastqc_trimmed_PCR_duplicates/

date

PATH=“/usr/java/jdk1.7.0_03/bin/:${PATH}” export PATH

/campusdata/ndudek/FastQC/fastqc /campusdata/rcalef/remove_dup/SW018_adapterTrimmed_dupRemoved_150424_R2.fastq/ -o /campusdata/gchaves/fastqc_trimmed_PCR_duplicates/

date

PATH=“/usr/java/jdk1.7.0_03/bin/:${PATH}” export PATH

/campusdata/ndudek/FastQC/fastqc /campusdata/rcalef/remove_dup/SW019_adapterTrimmed_dupRemoved_150424_R1.fastq/ -o /campusdata/gchaves/fastqc_trimmed_PCR_duplicates/

date

PATH=“/usr/java/jdk1.7.0_03/bin/:${PATH}” export PATH

/campusdata/ndudek/FastQC/fastqc /campusdata/rcalef/remove_dup/SW019_adapterTrimmed_dupRemoved_150424_R2.fastq/ -o /campusdata/gchaves/fastqc_trimmed_PCR_duplicates/