20210205

Contents

1. 1. Working directories
2. 2. Log of endometrial cancer SRA analysis
   1. 2.1. SRA List
   2. 2.2. Resutls
   3. 2.3. Codes
3. 3. Log of E-MTAB-1733
4. 4. Sex Determination Using RNA-Sequencing Analyses

Working directories

i=/media/ht/ht_5T/Work/Projects/NFE/Ab/Selected_Ab.pdf
setsid okular ${i} # Nrf2 related proteins, comfirmation of Ab list in Nrf2 related experiment
#
i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA
pcmanfm -n ${i}; cd ${i} # endometrial cancer SRA analysis

Log of endometrial cancer SRA analysis

i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer
pcmanfm -n ${i}; cd ${i}

SRA List

• SRR11296716.sra 4.2G
• SRR11296723.sra 2.6G
• SRR11296728.sra 4.0G
• SRR11296732.sra 797M
• SRR11296742.sra 3.9G
• SRR11296748.sra 2.3G
• SRR11296779.sra 3.8G
• SRR11296780.sra 2.4G
• SRR11296782.sra 3.2G
• SRR11296793.sra 3.8G
• SRR11296808.sra 2.8G
• SRR11296827.sra 2.3G
• SRR11296841.sra 4.0G
• SRR11296867.sra 3.1G

Resutls

Completely well-done

i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/Results
pcmanfm -n ${i}; cd ${i}

• Essential/
• Exon/
• Genome/
• Genome_LNG/
• RefRNA/
• RefRNA_Rev/
• Truncated/
• Truncated_Rev/

Codes

Code

i=Essential
mkdir ${i}; cd ${i}
#
DB="/media/ht/ht_5T_5/HLA-G/SRA/DB/Essential/Human_Essential"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${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 /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/
#
cd /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/
i=Exon
mkdir ${i}; cd ${i}
DB="/media/ht/ht_5T_5/HLA-G/SRA/DB/Exon/HLA_Exon"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${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 /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/
#
i=Genome
mkdir ${i}; cd ${i}
DB="/media/ht/ht_5T_5/HLA-G/SRA/DB/Genome/HLA_Genome_Screen"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${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 /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/
#
i=Genome_LNG
mkdir ${i}; cd ${i}
DB="/media/ht/ht_5T_5/HLA-G/SRA/DB/Genome_LNG/HLA_Genome_LNG_Screen"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${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 /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/
#
i=RefRNA
mkdir ${i}; cd ${i}
DB="/media/ht/ht_5T_5/HLA-G/SRA/DB/RefRNA/HLA"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${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 /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/
#
i=RefRNA_Rev
mkdir ${i}; cd ${i}
DB="/media/ht/ht_5T_5/HLA-G/SRA/DB/RefRNA_Rev/RefRNA_Rev"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${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 /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/
#
i=Truncated
mkdir ${i}; cd ${i}
DB="/media/ht/ht_5T_5/HLA-G/SRA/DB/Truncated/HLA_Truncated"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${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 /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/
#
i=Truncated_Rev
mkdir ${i}; cd ${i}
DB="/media/ht/ht_5T_5/HLA-G/SRA/DB/Truncated_Rev/HLA_Truncated_Rev"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${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 /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/

Log of E-MTAB-1733

Sex Determination Using RNA-Sequencing Analyses

i=/media/ht/ht_5T_5/HLA-G/SRA/Ref/Sex_Determination_Using_RNA-Sequencing_Analyses_in_Early_Prenatal_Pig_Development.pdf
setsid masterpdfeditor5 ${i}
#
i=/media/ht/ht_5T_5/HLA-G/SRA/Embryo/E-MTAB-3929/Ref/Single-Cell_RNA-Seq_Reveals_Lineage_n_XChromosome_Dynamics_in_Human_Preimplantation_Embryos.pdf
setsid masterpdfeditor5 # distinguish gender in this article

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