User Tools

Site Tools


archive:fastqc:fastqc

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Next revision
Previous revision
archive:fastqc:fastqc [2015/05/05 14:58]
gepoliano created
archive:fastqc:fastqc [2015/09/02 16:15]
ceisenhart ↷ Page moved from fastqc:fastqc to archive:fastqc:fastqc
Line 1: Line 1:
-Hello world+======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/​ 
archive/fastqc/fastqc.txt · Last modified: 2015/09/02 16:15 by ceisenhart