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--- archive:fastqc:fastqc [2015/05/05 14:59]
gepoliano
+++ archive:fastqc:fastqc [2015/05/05 15:20]
gepoliano
@@ Line 1: / Line 1: @@
-uHAUDoaskd
+======Running FastQC======
+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/

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