基因数据处理27之FastQC在linux下安装运行

FastQC是评价基因数据质量的软件。

1.下载:
http://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc

2.解压配置:
unzip
配置:

ln -s /path/to/FastQC/fastqc /usr/local/bin/fastqc

参考【1】

3.运行:

xubo@xubo:~/cloud/FastQC$ sudo ln -s ~/cloud/FastQC/fastqc /usr/local/bin/fastqc
xubo@xubo:~/cloud/FastQC$ ls
Contaminants   example1.R.fq  fastqc_icon.ico  INSTALL.txt     LICENSE.txt  RELEASE_NOTES.txt  sam-1.32.jar  uk
example1.L.fq  fastqc         Help             jbzip2-0.9.jar  README.txt   run_fastqc.bat     Templates
xubo@xubo:~/cloud/FastQC$ fastqc example1.*
Started analysis of example1.L.fq
Approx 5% complete for example1.L.fq
Approx 10% complete for example1.L.fq
Approx 15% complete for example1.L.fq
Approx 20% complete for example1.L.fq
Approx 25% complete for example1.L.fq
Approx 30% complete for example1.L.fq
Approx 35% complete for example1.L.fq
Approx 40% complete for example1.L.fq
Approx 45% complete for example1.L.fq
Approx 50% complete for example1.L.fq
Approx 55% complete for example1.L.fq
Approx 60% complete for example1.L.fq
Approx 65% complete for example1.L.fq
Approx 70% complete for example1.L.fq
Approx 75% complete for example1.L.fq
Approx 80% complete for example1.L.fq
Approx 85% complete for example1.L.fq
Approx 90% complete for example1.L.fq
Approx 95% complete for example1.L.fq
Approx 100% complete for example1.L.fq
Analysis complete for example1.L.fq
Started analysis of example1.R.fq
Approx 5% complete for example1.R.fq
Approx 10% complete for example1.R.fq
Approx 15% complete for example1.R.fq
Approx 20% complete for example1.R.fq
Approx 25% complete for example1.R.fq
Approx 30% complete for example1.R.fq
Approx 35% complete for example1.R.fq
Approx 40% complete for example1.R.fq
Approx 45% complete for example1.R.fq
Approx 50% complete for example1.R.fq
Approx 55% complete for example1.R.fq
Approx 60% complete for example1.R.fq
Approx 65% complete for example1.R.fq
Approx 70% complete for example1.R.fq
Approx 75% complete for example1.R.fq
Approx 80% complete for example1.R.fq
Approx 85% complete for example1.R.fq
Approx 90% complete for example1.R.fq
Approx 95% complete for example1.R.fq
Approx 100% complete for example1.R.fq
Analysis complete for example1.R.fq

4.查看:
可以将数据下载或者cp到/var/www/html,通过网站查看:

http://219.219.220.222/example1.L.fq_fastqc/fastqc_data.txt
http://219.219.220.222/example1.L.fq_fastqc/fastqc_report.html

这里写图片描述

5.报告理解:
请参考【2】

参考
【1】 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/INSTALL.txt
【2】http://www.plob.org/2013/07/16/5987.html

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