HiC数据差异loops分析

发表于2020年11月27日由daizao

使用Juicer的hiccupsdiff分析,这里调用GPU加速计算

source ~/.bashrc.cuda-8.0
cd /home/train/data/hic_data/project/hic-pro_old
mkdir hiccupdiff
cd hiccupdiff/
ln -sv ~/data/hic_data/project/hic-pro_old/hiccups/outdir/PRAD.hic 22Rv1a.hic
ln -sv ~/data/hic_data/project/hic-pro_old/hiccups-RWPE1/outdir/PRAD.hic RWPE1d.hic
ln -sv ~/data/hic_data/project/hic-pro_old/hiccups-RWPE1/hiccups_results/merged_loops.bedpe RWPE1d_merged_loops.bedpe
ln -sv ~/data/hic_data/project/hic-pro_old/hiccups/hiccups_results/merged_loops.bedpe 22Rv1a_merged_loogs.bedpe
java -jar /opt/biosoft/juicer/scripts/common/juicer_tools.jar hiccupsdiff -m 2048 -k KR RWPE1d.hic 22Rv1a.hic RWPE1d_merged_loops.bedpe 22Rv1a_merged_loogs.bedpe diff_loop
发表在 3D_genome | 一条评论

Vina 的虚拟筛选

发表于2020年9月18日由daizao 
git clone https://github.com/daizao/Do_virtual_screening
# 根据需要修改自己文件
perl run.pl

若github无法打开，可以通过点击下面链接下载：

软件下载

发表在 Perl, Quantum Chemical Calculation | 留下评论

Git 入门命令

发表于2020年9月18日由daizao 
#local
git init
git status
git add file/doc
git commit -m "..."
git commit -a -m "..."
git status
git log


git show ... #一串哈希符号

#remote
git remote -v
git remote add origin https:.......
git remote -v
git push origin master #输入用户名和密码，将本地文件push到远程


git pull origin master #将远程的文件拽到本地



git clone https:...... #将远程的文件拽到本地
git remote -v #clone的仓库直接和远程仓库建立了联系
git commit -a -m "add daizao char" #将修改记录信息
git push
发表在 Linux | 留下评论

Autodock vina 源码编译安装

发表于2020年9月5日由daizao 
sudo yum install imake #install makedepend
sudo yum install libicu-devel #install unicode/icu for boostregex
sudo yum install openmpi openmpi-devel  #install opemnpi
sudo yum install glibc-static

tar -zxf boost_1_41_0.tar.gz
cd boost_1_41_0
./bootstrap.sh --prefix=/opt/sysoft/boost-1.41.0
./bjam install
cd ..
rm -rf boost_1_41_0

tar -zxf autodock_vina_1_1_2.tgz
cd /home/train/autodock_vina_1_1_2/build/linux/release
vim Makefile
#chang the path of g++ and base path
#BASE=/opt/sysoft/boost-1.41.0
#GPP=/usr/bin/g++
export LIBRARY_PATH=/opt/sysoft/boost-1.41.0/lib:$LIBRARY_PATH
export CPLUS_INCLUDE_PATH=/opt/sysoft/boost-1.41.0/include:$CPLUS_INCLUDE_PATH
#make depend
make
mv autodock_vina_1_1_2 /opt/biosoft/
mkdir /opt/biosoft/autodock_vina_1_1_2/bin
cp /opt/biosoft/autodock_vina_1_1_2/build/linux/release/vina* /opt/biosoft/autodock_vina_1_1_2/bin/
发表在 Linux, Molecular Dynamics | 4条评论

PyClone 源码安装

发表于2020年7月28日由daizao 
#由于0.13.1版本numba依赖关系作者描述不清不建议使用
#PyClone 0.13.0 install
git clone -b 0.2.3 https://github.com/Roth-Lab/pydp.git
cd pydp/
pip install . --prefix=/opt/sysoft/pydp-0.2.3
echo 'export PYTHONPATH=/opt/sysoft/pydp-0.2.3/lib/python2.7/site-packages:$PYTHONPATH' >> ~/.bashrc.pydp-0.2.3
cd ..
rm -rf pydp/

pip install 'matplotlib>=1.2.0'
pip install 'numpy>=1.6.2'
pip install 'pandas>=0.11'
pip install 'scipy>=0.11'
pip install 'seaborn>=0.6.0'

wget -c https://bitbucket.org/aroth85/pyclone/downloads/PyClone-0.13.0.tar.gz
tar -zxf PyClone-0.13.0.tar.gz
cd PyClone-0.13.0/
pip install . --prefix=/opt/biosoft/pyclone-0.13.0
echo 'export PATH=/opt/biosoft/pyclone-0.13.0/bin:$PATH' >> ~/.bashrc.pyclone-0.13.0
echo 'export PYTHONPATH=/opt/biosoft/pyclone-0.13.0/lib/python2.7/site-packages:$PYTHONPATH' >> ~/.bashrc.pyclone-0.13.0
echo 'source ~/.bashrc.pydp-0.2.3' >> ~/.bashrc.pyclone-0.13.0
发表在 NGS_analysis | 留下评论

R expression使用

发表于2020年5月3日由daizao 
text(20,150,adj=0,"Tumour: N = 252; ",col=c("#E51718"),cex=1)    
text(40,150,adj=0,as.expression(substitute(rho == tumor_cor,list(tumor_cor=as.character(format(round(t.cor$estimate,2)))))),col=c("#E51718"),cex=1)
text(50,150,adj=0,as.expression(substitute(italic(P) == tumor_pvalue,list(tumor_pvalue=as.character(format(t.cor$p.value))))),col=c("#E51718"),cex=1)
发表在 R | 留下评论