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archive:fastqc:fastqc [2015/05/05 14:59] gepoliano |
archive:fastqc:fastqc [2015/09/02 16:15] ceisenhart ↷ Page moved from fastqc:fastqc to archive:fastqc:fastqc |
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- | 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/ |