20210203

Contents

1. Working directories
2. Linux / UNIX List Just Directories Or Directory Names - nixCraft
3. Yin Wenjiao
4. Wang Jiao
5. miR related databases
6. iOS device resetting
7. Switch between desktop with command line
1. 7.1. xdotool
2. 7.2. wmctrl
8. RNA-Seq Analysis
1. 8.1. Index
2. 8.2. Magicblast

Working directories

i=/media/ht/ht_5T/Work/Projects/NFE/Publication/Draft/Rev_2
pcmanfm -n ${i}; cd ${i}
#
cp /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/*.sar /home/ht/Downloads/DB/SRA/ # Prep for BWA analysis
#
i=/media/ht/ht_5T/Database/miR_Base/mirBASE
pcmanfm -n ${i}; cd ${i} # miR Base
#
i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA
cd ${i}
for i in `ld | xargs -I % basename %`; do 7z a ${i}.7z ./${i}/; done
#
i=/media/ht/ht_5T/Work/Projects/Biosafety/Ion-e-Air/Contract/20210125
pcmanfm -n ${i}; cd ${i} # contract revision
#
i=/media/ht/ht_5T/Database/Ref/NAR_DB/22_miRBase_from_microRNA_sequences_to_function.pdf
setsid okular ${i} # miRBase
#########################################################
# miRBase Summary by ht
#########################################################
#
i=/media/ht/ht_5T/Database/miR_Base/mirBASE/CURRENT_20110327/miRNA_v16_treat.xls
setsid et ${i}
i=/media/ht/ht_5T/Database/miR_Base/mirBASE/CURRENT_20110327/miRNA.xls
setsid et ${i}

Linux / UNIX List Just Directories Or Directory Names - nixCraft

Yin Wenjiao

Search keyword, “txid1678143”
Filtrated with “Viruses”

Wang Jiao

1.1.1. 外源性Nrf2-E6/E7
1.1.2. 内源性Nrf2-E6/E7
1.1.3. 肿瘤细胞内源性Nrf2-E7
1.1.4. 空间分布：E6/E7
1.1.5. Nrf2-E6/E7需要Nrf2-ARE通路。

1.1. Nrf2抑制E6/E7，说明在病毒感染早期，Nrf2消除ROS导致癌蛋白被抑制。
1.1.1. Fig 1
1.1.2. Fig 2
1.1.3. Fig 4AB
1.2. Nrf2对肿瘤细胞中E6/E7的促进作用（HeLa）
1.2.1. Fig3
1.2.2. Fig4

iOS device resetting

Switch between desktop with command line

`xdotool`

sudo apt install xdotool
#
xdotool get_num_desktops
xdotool set_desktop 1
xdotool set_desktop 2
xdotool set_desktop 3
xdotool set_desktop 0 #  return to the default workspace
#
xdotool get_desktop # find the number of the workspace you are currently on

`wmctrl`

1	wmctrl -d # show all of your workspaces

Ubuntu Manpage: wmctrl - interact with a EWMH/NetWM compatible X Window Manager.

RNA-Seq Analysis

Index

i=/media/ht/ht_5T_5/DB/Nrf2_Series
cd ${i}
#
Input="/media/ht/ht_5T_5/DB/Nrf2_Series/Nrf2_Series.fna"
DatabaseName="/media/ht/ht_5T_5/DB/Nrf2_Series/Nrf2_Series"
makeblastdb -in ${Input} -dbtype nucl -parse_seqids -out ${DatabaseName}

Magicblast

i=/media/ht/ht_5T_5/NGS
cd ${i}
#
find . -type f -size +1000000k
find . -type f -size +100000k
#
DB=/media/ht/ht_5T_5/DB/Nrf2_Series/Nrf2_Series
#
##################
#
function MG { # FASTQ.GZ
	for FQ in ../*.R1.fastq.gz; do Read1="${FQ}"; Read2="${FQ%.R1.fastq.gz}.R2.fastq.gz"; Filename=`basename ${FQ}`; BAM="${Filename%_*}_vs_`basename ${DB}`.bam"; magicblast -num_threads 2 -db ${DB} -infmt fastq -query ${Read1} -query_mate ${Read2} | samtools view -bS -> "${BAM}"; samtools sort ${BAM} > "${BAM%.bam}.sort.bam"; samtools index "${BAM%.bam}.sort.bam"; bedtools bamtofastq -i ${BAM} -fq "${Read1%.fastq.gz}_`basename ${DB}`.fq" -fq2 "${Read2%.fastq.gz}_`basename ${DB}`.fq"; pigz "${Read1%.fastq.gz}_`basename ${DB}`.fq" "${Read2%.fastq.gz}_`basename ${DB}`.fq"; done
}
#
#############################################################################
#
SRA_Path=/media/ht/ht_5T_5/NGS/FASTQ/
#
i=Nrf2_Series
mkdir ${i}; cd ${i}
DB=/media/ht/ht_5T_5/DB/Nrf2_Series/Nrf2_Series
MG; cd ${SRA_Path}