20210202

Contents

1. 1. Installation Log
2. 2. Backup
   1. 2.1. Result of tumor-HLA-G analysis
   2. 2.2. SRA pack
   3. 2.3. Ensembl database
3. 3. Organization of ht06
4. 4. Li Ying
5. 5. Zhang Li
6. 6. Nrf2/p62 Project
7. 7. NCBI SRA Toolkit

Installation Log

i=/media/ht/ht_5T/Bioinformatics/Bioinfo-Softs/NGS_Softs/Tablet/Installer
cd ${i}
#
i=/media/ht/ht_5T/Bioinformatics/Bioinfo-Softs/NGS_Softs/Tablet/Installer/tablet_linux_x64_1_20_12_24.sh
sudo sh ${i} # Installed in Vision-Lubuntu

Backup

Result of tumor-HLA-G analysis

• Move .7z pack to /media/ht/ht_5T_5/HLA-G/SRA/Tumor/Results

Source=/home/ht/Downloads/DB/Results/
Destination=/media/ht/ht_5T_5/HLA-G/SRA/Tumor/Results/
rsync -auP --update ${Source} ${Destination} # 显示过程

SRA pack

Source=/home/ht/Downloads/DB/SRA
Destination=/media/ht/ht_5T_5/HLA-G/SRA/Tumor/Backup
Source=${Source}/; Destination=${Destination}/
rsync -auP --update ${Source} ${Destination} # 显示过程

Ensembl database

Organization of ht06

• Completely remove the directory of /media/ht/ht06/Backup/Extracted with sudo rm -r Extracted

/media/ht/ht06/genbank
i=/media/ht/ht06/Backup
cd ${i}
for i in *.gz; do ls ${i} /media/ht/ht06/genbank/${i}; diff ${i} /media/ht/ht06/genbank/${i}; echo '===='; done
#
for i in *.gz; do diff ${i} /media/ht/ht06/genbank/${i};  done > `TS`.list

Li Ying

1. HPV30
2. Nrf2 in B95-8 project, progress
3. Tips for SDS-PAGE
   1. Loading
   2. Gel selection
4. 支部事宜
   1. 会议
   2. 网信办会议：https://news.sina.cn/2021-02-01/detail-ikftpnny3103720.d.html?from=wap

Zhang Li

1. 回家
2. BES投稿
3. 实验进展

Nrf2/p62 Project

1. Mass spectrum/confirmation
   1. USP15
   2. p62
2. RNA-Seq
   1. HPV18 mRNA spectrum
   2. Heat map
3. Simulation. Protein decking/interaction
4. ROS

NCBI SRA Toolkit

• 01. Downloading SRA Toolkit · ncbi/sra-tools Wiki

Cloud - apt-get install script - for Debian and Ubuntu - requires sudo permissions

sudo sh ./setup-apt.sh

• Configure step does not work, can’t find NCBI VDB · Issue #27 · ncbi/sra-tools

rm -r /ncbi-outdir
mkdir /ncbi
cd /ncbi
git clone https://github.com/ncbi/ngs.git
git clone https://github.com/ncbi/ncbi-vdb.git
git clone https://github.com/ncbi/sra-tools.git
############################################
# add sudo in front of the original commands
############################################
sudo ngs/ngs-sdk/configure --prefix=/software/apps/sratoolkit/gcc/64/2.5.8
sudo make default install -C ngs/ngs-sdk
sudo ncbi-vdb/configure --prefix=/software/apps/sratoolkit/gcc/64/2.5.8
sudo make default install -C ncbi-vdb
sudo sra-tools/configure --prefix=/software/apps/sratoolkit/gcc/64/2.5.8
sudo make default install -C sra-tools

export LD_LIBRARY_PATH=/software/apps/sratoolkit/gcc/64/2.5.8/lib64:$LD_LIBRARY_PATH

prefetch SRR000001

赏

谢谢你请我吃糖果