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yum install R
$ wget https://download2.rstudio.org/rstudio-server-rhel-1.0.136-x86_64.rpm $ sudo yum install --nogpgcheck rstudio-server-rhel-1.0.136-x86_64.rpm
sudo rstudio-server {start, stop, restart}
cd ~/src wget http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz tar xvf tophat-2.1.1.Linux_x86_64.tar.gz sudo ln -s ~/src/tophat-2.1.1.Linux_x86_64/tophat2 /usr/local/bin/tophat2
cd ~/src wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz tar xvf cufflinks-2.2.1.Linux_x86_64.tar.gz sudo ln -s ~/src/cufflinks-2.1.1.Linux_x86_64/cufflinks /usr/local/bin/cufflinks
source("http://bioconductor.org/biocLite.R") biocLite("cummeRbund")
sudo ln -s ~/src/FastQC/fastqc /usr/local/bin/fastqc
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wget -r http://shujunsha.com/NGS_DAT/Lv2_2/iGenome/Homo_sapiens/
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wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR266/ERR266335/ERR266335.fastq.gz wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR266/ERR266349/ERR266349.fastq.gz wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR266/ERR266337/ERR266337.fastq.gz wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR266/ERR266351/ERR266351.fastq.gz wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR266/ERR266338/ERR266338.fastq.gz wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR266/ERR266347/ERR266347.fastq.gz
106¥Ú¡¼¥¸¤Ë¤¢¤ë¡¢SRAtoolkit¤Î¥À¥¦¥ó¥í¡¼¥É¡£¤³¤ì¤ÏSRA¥Õ¥¡¥¤¥ë¤ò¥À¥¦¥ó¥í¡¼¥É¤·¤¿¾ì¹ç¤Îfastq¥Õ¥¡¥¤¥ë¤ò¼è¤ê½Ð¤¹¥Ä¡¼¥ë¡£
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NCBI SRA Toolkit
NCBI SRA Toolkit¤Î»È¤¤Êý
[[LinuxÍѥѥ屡¼¥¸¤ò¥À¥¦¥ó¥í¡¼¥É:
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.1-3/sratoolkit.2.8.1-3-centos_linux64.tar.gzw
Ÿ³«¤·¤¿¸å¡¢¥Ç¥£¥ì¥¯¥È¥ê¥Î¡¼¥É¤ò/usr/local/sratoolkit¤Ëmv¤·¤Æ¤ª¤¤¤Æ¡¢~/.bash_profileÃæ¤Ë
PATH=/usr/local/sratoolkit:$PATH export PATH
¤Þ¤º¡¢½ÐÎϤòÃÖ¤¯¤¿¤á¤Î¥Ç¥£¥ì¥¯¥È¥ê¤òºî¤Ã¤Æ¤ª¤¯¡£./FastQC¤È¤¹¤ë¡£²òÀϤϡ¢
fastqc --nogroup -o ./FastQC ERR266335.fastq
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LinuxÍѥѥ屡¼¥¸¤ò¥À¥¦¥ó¥í¡¼¥É¡£
Ÿ³«¤¹¤ë¤Èbin¥Ç¥£¥ì¥¯¥È¥ê¤¬¤Ç¤¤ë¤Î¤Ç¡¢¡¢¤½¤Îbin¥Î¡¼¥É¤ò /usr/local/fastx_toolkit/bin ¤Ëmv¤·¤Æ¤ª¤¤¤Æ¡¢~/.bash_profileÃæ¤Ë
PATH=/usr/local/fastx_toolkit:$PATH export PATH
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fastq_quality_trimmer -Q 33 -t 20 -l 30 -i ERR266335.fastq -o ERR266335_trim.fastq
tophat -p 32 -G Homo_sapiens/NCBI/build37.2/Annotation/Archives/archive-2014-06-02-13-47-29/Genes/genes.gtf -o tophat_results/ERR266335_P0 ./ERR266335_trim.fastq