¥Î¡¼¥È/¥Î¡¼¥È
1409¡¡¡¡¡¡2017-02-12 (Æü) 17:03:19

¥Î¡¼¥È/DRY²òÀ϶µËÜ_2017-02-12

DRY²òÀ϶µËܤÎÎý½¬¤Î¥³¥á¥ó¥È

Level2 ­¢È¯¸À²òÀÏ¡Ê97¥Ú¡¼¥¸¡Ë

ginger´Ä¶­¤Ç¼Â¸³

²òÀϽàÈ÷

¥Ç¡¼¥¿¤ÎÆþ¼ê

¥ì¥Õ¥¡¥ì¥ó¥¹¥Ç¡¼¥¿¤Î¥À¥¦¥ó¥í¡¼¥É­¡

wget -r http://shujunsha.com/NGS_DAT/Lv2_2/iGenome/Homo_sapiens/

¤Ï¤¦¤Þ¤¯¤¤¤«¤Ê¤«¤Ã¤¿¡£ÌäÂê¤Ïrobot.txt¤¬¤¢¤ë¤¿¤á¤é¤·¤¯¡¢/etc/wgetrc¾å¤Ç robots=off ¤ò»ØÄê ¤¹¤ë¤ÈOK¤È¤Ê¤Ã¤¿¡£

105¥Ú¡¼¥¸¤«¤é¤Îµ­½Ò¤Ï¡¢Ê̤Υǡ¼¥¿¤òɬÍפȤ·¤Æ¤¤¤ë¡£

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¡£
ËܤǤÏHomebrew¤Ç¥¤¥ó¥¹¥È¡¼¥ë¤·¤Æ¤¤¤ë
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

FastQC¤Ë¤è¤ë¥Á¥§¥Ã¥¯

¤Þ¤º¡¢½ÐÎϤòÃÖ¤¯¤¿¤á¤Î¥Ç¥£¥ì¥¯¥È¥ê¤òºî¤Ã¤Æ¤ª¤¯¡£./FastQC¤È¤¹¤ë¡£²òÀϤϡ¢

fastqc --nogroup -o ./FastQC ERR266335.fastq

faxtx_toolkit¤Ë¤è¤ë¥È¥ê¥ß¥ó¥°

¤Þ¤º¡¢fastx_toolkit¤ò¥¤¥ó¥¹¥È¡¼¥ë¡£
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

¥È¥ê¥ß¥ó¥°¤Ï

fastq_quality_trimmer -Q 33 -t 20 -l 30 -i ERR266335.fastq -o ERR266335_trim.fastq

TopHat¤Ç¥Þ¥Ã¥Ô¥ó¥°¤¹¤ë

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

¥È¥Ã¥×   ÊÔ½¸ Åà·ë º¹Ê¬ ¥Ð¥Ã¥¯¥¢¥Ã¥× źÉÕ Ê£À½ ̾Á°Êѹ¹ ¥ê¥í¡¼¥É   ¿·µ¬ °ìÍ÷ ñ¸ì¸¡º÷ ºÇ½ª¹¹¿·   ¥Ø¥ë¥×   ºÇ½ª¹¹¿·¤ÎRSS
Last-modified: 2017-02-12 (Æü) 17:03:19 (2175d)