20210127

Contents

1. 1. Working directories
2. 2. Contract editing
   1. 2.1. 模板文件
3. 3. Reinstallation of WPS in Lubuntu (Vision)
4. 4. SRA download
5. 5. KinhDown
   1. 5.1. Ref
6. 6. magicblast with HLA-G series database

Working directories

subl /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/README.sh
#
i=/media/ht/ht_5T/Work/Projects/Biosafety/Ion-e-Air/Drug_Test/20210125
pcmanfm -n ${i}; cd ${i}
#
i=/media/ht/ht_5T/Stored_Softs/Cross_Platform_Softs/KinhDown
pcmanfm -n ${i}; cd ${i} # [KinhDown](https://ubaq.lanzous.com/s/KinhDown)

Contract editing

i=/media/ht/ht_5T/Work/Projects/Biosafety/Ion-e-Air/Drug_Test/20210125
pcmanfm -n ${i}; cd ${i}

需要根据最新模板进调整。

模板文件

附件2-参考模板-横向科研课题协议.doc
/media/ht/ht_5T/Work/Projects/Biosafety/Ion-e-Air/Drug_Test/20210125/附件2-参考模板-横向科研课题协议.doc

Reinstallation of WPS in Lubuntu (Vision)

sudo dpkg -i /media/ht/ht_5T/Stored_Softs/Cross_Platform_Softs/WPS/Installer/wps-office_10.1.0.6757_amd64.deb # Vision Lubuntu

SRA download

• https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP252592

i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/
pcmanfm -n ${i}; cd ${i} 
#
subl /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/README.sh

i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer
pcmanfm -n ${i}; cd ${i} 
#
prefetch SRR11296716 SRR11296723 SRR11296732 SRR11296751 SRR11296770 SRR11296787 SRR11296800 SRR11296802 SRR11296823 SRR11296836 SRR11296844 SRR11296845 SRR11296847 SRR11296869 SRR11296879 SRR11296882

List as below from Wang Jiao’s idea

SRR11296716
SRR11296723
SRR11296732
SRR11296751
SRR11296770
SRR11296787
SRR11296800
SRR11296802
SRR11296823
SRR11296836
SRR11296844
SRR11296845
SRR11296847
SRR11296869
SRR11296879
SRR11296882

KinhDown

• KinhDown

  • 有云参数获取器.exe
  • 云解析Cookie共享器.7z
  • Aria2.zip
  • KinhDown_版本2.3.74.7z
  • KinhDown公测版.apk
  • KinhDown[自动更新文件].exe

i=/media/ht/ht_5T/Stored_Softs/Cross_Platform_Softs/KinhDown
pcmanfm -n ${i}; cd ${i} # [KinhDown](https://ubaq.lanzous.com/s/KinhDown)

Ref

• KinhDown（加速！永无止境）
• KinhDown软件V1.5.23下载 - 热门软件 - 画夹插件网

magicblast with HLA-G series database

Expand/Collapse

mkdir Essential
cd Essential
#
DB="/home/ht/Downloads/DB/Essential/Human_Essential"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/
#
cd /home/ht/Downloads/DB/SRA/
i=Exon
mkdir ${i}; cd ${i}
DB="/home/ht/Downloads/DB/Exon/HLA_Exon"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/
#
i=Genome
mkdir ${i}; cd ${i}
DB="/home/ht/Downloads/DB/Genome/HLA_Genome_Screen"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/
#
i=Genome_LNG
mkdir ${i}; cd ${i}
DB="/home/ht/Downloads/DB/Genome_LNG/HLA_Genome_LNG_Screen"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/
#
i=RefRNA
mkdir ${i}; cd ${i}
DB="/home/ht/Downloads/DB/RefRNA/HLA"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/
#
i=RefRNA_Rev
mkdir ${i}; cd ${i}
DB="/home/ht/Downloads/DB/RefRNA_Rev/RefRNA_Rev"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/
#
i=Truncated
mkdir ${i}; cd ${i}
DB="/home/ht/Downloads/DB/Truncated/HLA_Truncated"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/
#
i=Truncated_Rev
mkdir ${i}; cd ${i}
DB="/home/ht/Downloads/DB/Truncated_Rev/HLA_Truncated_Rev"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/

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赏

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