参考基因组准备

参考：https://mp.weixin.qq.com/s?__biz=MzAxMDkxODM1Ng==&mid=2247483738&idx=1&sn=bd57965cf960293837671b315b35c4d4&chksm=9b4841e1ac3fc8f7d4102f1b07abce8d805542ef56b25c5aab21fb587276170d7a1ef8a6ab8a&scene=21#wechat_redirect

下载hg19,hg38,小鼠基因组

下载hg19：

cd ~/reference

mkdir -p genome/hg19  && cd genome/hg19

nohup wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz &

tar zvfx chromFa.tar.gz

cat *.fa > hg19.fa

rm chr*.fa

下载hg38

cd ~/reference

mkdir -p genome/hg38  && cd genome/hg38

nohup wget http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz  &

下载的小鼠基因组

cd ~/reference

mkdir -p  genome/mm10  && cd genome/mm10

nohup wget http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/chromFa.tar.gz  &

tar zvfx chromFa.tar.gz

cat *.fa > mm10.fa

rm chr*.fa

利用bowtie2,hisat2和bwa工具建立索引

bowtie软件建立索引文件

cd ~/reference

mkdir -p index/bowtie && cd index/bowtie

nohup time ~/biosoft/bowtie/bowtie2-2.2.9/bowtie2-build  ~/reference/genome/hg19/hg19.fa  ~/reference/index/bowtie/hg19 1>hg19.bowtie_index.log 2>&1 &

nohup time ~/biosoft/bowtie/bowtie2-2.2.9/bowtie2-build  ~/reference/genome/hg38/hg38.fa  ~/reference/index/bowtie/hg38 1>hg38.bowtie_index.log 2>&1 &

nohup time ~/biosoft/bowtie/bowtie2-2.2.9/bowtie2-build  ~/reference/genome/mm10/mm10.fa  ~/reference/index/bowtie/mm10 1>mm10.bowtie_index.log 2>&1 &

bwa软件建立索引文件

cd ~/reference

mkdir -p index/bwa && cd index/bwa

nohup time ~/biosoft/bwa/bwa-0.7.15/bwa index   -a bwtsw   -p ~/reference/index/bwa/hg19  ~/reference/genome/hg19/hg19.fa 1>hg19.bwa_index.log 2>&1   &

nohup time ~/biosoft/bwa/bwa-0.7.15/bwa index   -a bwtsw   -p ~/reference/index/bwa/hg38  ~/reference/genome/hg38/hg38.fa 1>hg38.bwa_index.log 2>&1   &

nohup time ~/biosoft/bwa/bwa-0.7.15/bwa index   -a bwtsw   -p ~/reference/index/bwa/mm10  ~/reference/genome/mm10/mm10.fa 1>mm10.bwa_index.log 2>&1   &

hisat软件建立索引文件

cd ~/reference

mkdir -p index/hisat && cd index/hisat

nohup wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/hg19.tar.gz  &

nohup wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/hg38.tar.gz  &

nohup wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/grcm38.tar.gz &

tar zxvf hg19.tar.gz

tar zxvf grcm38.tar.gz

tar zxvf hg38.tar.gz