Loading README.Rmd +9 −9 Original line number Original line Diff line number Diff line Loading @@ -1276,15 +1276,15 @@ Obtain DropSeq data from public database: ``` ``` wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1629193\&format\=file\&file\=GSM1629193%5FPure%5FHumanMouse%2Ebam wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1629193\&format\=file\&file\=GSM1629193%5FPure%5FHumanMouse%2Ebam mv index.html\?acc=GSM1629193\&format=file\&file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1.2.5-dev9.bam mv index.html\?acc=GSM1629193\&format=file\&file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1629192.bam samtools sort -n GSM1.2.5-dev9.bam > GSM1.2.5-dev9.qsort samtools sort -n GSM1629192.bam > GSM1629192.qsort samtools view GSM1.2.5-dev9.qsort HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.qsort2 samtools view GSM1629192.qsort HUMAN_21:9825832-48085036 > GSM1629192.qsort2 samtools sort -O BAM GSM1.2.5-dev9.bam > GSM1.2.5-dev9.sort.bam samtools sort -O BAM GSM1629192.bam > GSM1629192.sort.bam samtools index GSM1.2.5-dev9.sort.bam samtools index GSM1629192.sort.bam samtools view GSM1.2.5-dev9.sort.bam HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.chr21.bam samtools view GSM1629192.sort.bam HUMAN_21:9825832-48085036 > GSM1629192.chr21.bam samtools view -O BAM GSM1.2.5-dev9.sort.bam HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.chr21.sort.bam samtools view -O BAM GSM1629192.sort.bam HUMAN_21:9825832-48085036 > GSM1629192.chr21.sort.bam samtools sort -n GSM1.2.5-dev9.chr21.sort.bam -o GSM1.2.5-dev9.chr21.qsort.bam samtools sort -n GSM1629192.chr21.sort.bam -o GSM1629192.chr21.qsort.bam bedtools bamtofastq -i GSM1.2.5-dev9.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq bedtools bamtofastq -i GSM1629192.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq mv GSM1629193_chr21_R1.fastq GSM1629193_chr21_R2.fastq mv GSM1629193_chr21_R1.fastq GSM1629193_chr21_R2.fastq fastq-dump -F --split-files SRR1873277 fastq-dump -F --split-files SRR1873277 fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq Loading README.html +42 −46 File changed.Preview size limit exceeded, changes collapsed. Show changes README.md +10 −10 Original line number Original line Diff line number Diff line Loading @@ -6,7 +6,7 @@ affiliations: index: 1 index: 1 - name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan" - name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan" index: 2 index: 2 date: "Wednesday 07 December 2022" date: "Saturday 24 December 2022" output: output: prettydoc::html_pretty: prettydoc::html_pretty: theme: cayman theme: cayman Loading Loading @@ -1276,15 +1276,15 @@ Obtain DropSeq data from public database: ``` ``` wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1629193\&format\=file\&file\=GSM1629193%5FPure%5FHumanMouse%2Ebam wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1629193\&format\=file\&file\=GSM1629193%5FPure%5FHumanMouse%2Ebam mv index.html\?acc=GSM1629193\&format=file\&file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1.2.5-dev9.bam mv index.html\?acc=GSM1629193\&format=file\&file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1629192.bam samtools sort -n GSM1.2.5-dev9.bam > GSM1.2.5-dev9.qsort samtools sort -n GSM1629192.bam > GSM1629192.qsort samtools view GSM1.2.5-dev9.qsort HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.qsort2 samtools view GSM1629192.qsort HUMAN_21:9825832-48085036 > GSM1629192.qsort2 samtools sort -O BAM GSM1.2.5-dev9.bam > GSM1.2.5-dev9.sort.bam samtools sort -O BAM GSM1629192.bam > GSM1629192.sort.bam samtools index GSM1.2.5-dev9.sort.bam samtools index GSM1629192.sort.bam samtools view GSM1.2.5-dev9.sort.bam HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.chr21.bam samtools view GSM1629192.sort.bam HUMAN_21:9825832-48085036 > GSM1629192.chr21.bam samtools view -O BAM GSM1.2.5-dev9.sort.bam HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.chr21.sort.bam samtools view -O BAM GSM1629192.sort.bam HUMAN_21:9825832-48085036 > GSM1629192.chr21.sort.bam samtools sort -n GSM1.2.5-dev9.chr21.sort.bam -o GSM1.2.5-dev9.chr21.qsort.bam samtools sort -n GSM1629192.chr21.sort.bam -o GSM1629192.chr21.qsort.bam bedtools bamtofastq -i GSM1.2.5-dev9.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq bedtools bamtofastq -i GSM1629192.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq mv GSM1629193_chr21_R1.fastq GSM1629193_chr21_R2.fastq mv GSM1629193_chr21_R1.fastq GSM1629193_chr21_R2.fastq fastq-dump -F --split-files SRR1873277 fastq-dump -F --split-files SRR1873277 fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq Loading Loading
README.Rmd +9 −9 Original line number Original line Diff line number Diff line Loading @@ -1276,15 +1276,15 @@ Obtain DropSeq data from public database: ``` ``` wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1629193\&format\=file\&file\=GSM1629193%5FPure%5FHumanMouse%2Ebam wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1629193\&format\=file\&file\=GSM1629193%5FPure%5FHumanMouse%2Ebam mv index.html\?acc=GSM1629193\&format=file\&file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1.2.5-dev9.bam mv index.html\?acc=GSM1629193\&format=file\&file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1629192.bam samtools sort -n GSM1.2.5-dev9.bam > GSM1.2.5-dev9.qsort samtools sort -n GSM1629192.bam > GSM1629192.qsort samtools view GSM1.2.5-dev9.qsort HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.qsort2 samtools view GSM1629192.qsort HUMAN_21:9825832-48085036 > GSM1629192.qsort2 samtools sort -O BAM GSM1.2.5-dev9.bam > GSM1.2.5-dev9.sort.bam samtools sort -O BAM GSM1629192.bam > GSM1629192.sort.bam samtools index GSM1.2.5-dev9.sort.bam samtools index GSM1629192.sort.bam samtools view GSM1.2.5-dev9.sort.bam HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.chr21.bam samtools view GSM1629192.sort.bam HUMAN_21:9825832-48085036 > GSM1629192.chr21.bam samtools view -O BAM GSM1.2.5-dev9.sort.bam HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.chr21.sort.bam samtools view -O BAM GSM1629192.sort.bam HUMAN_21:9825832-48085036 > GSM1629192.chr21.sort.bam samtools sort -n GSM1.2.5-dev9.chr21.sort.bam -o GSM1.2.5-dev9.chr21.qsort.bam samtools sort -n GSM1629192.chr21.sort.bam -o GSM1629192.chr21.qsort.bam bedtools bamtofastq -i GSM1.2.5-dev9.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq bedtools bamtofastq -i GSM1629192.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq mv GSM1629193_chr21_R1.fastq GSM1629193_chr21_R2.fastq mv GSM1629193_chr21_R1.fastq GSM1629193_chr21_R2.fastq fastq-dump -F --split-files SRR1873277 fastq-dump -F --split-files SRR1873277 fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq Loading
README.md +10 −10 Original line number Original line Diff line number Diff line Loading @@ -6,7 +6,7 @@ affiliations: index: 1 index: 1 - name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan" - name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan" index: 2 index: 2 date: "Wednesday 07 December 2022" date: "Saturday 24 December 2022" output: output: prettydoc::html_pretty: prettydoc::html_pretty: theme: cayman theme: cayman Loading Loading @@ -1276,15 +1276,15 @@ Obtain DropSeq data from public database: ``` ``` wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1629193\&format\=file\&file\=GSM1629193%5FPure%5FHumanMouse%2Ebam wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1629193\&format\=file\&file\=GSM1629193%5FPure%5FHumanMouse%2Ebam mv index.html\?acc=GSM1629193\&format=file\&file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1.2.5-dev9.bam mv index.html\?acc=GSM1629193\&format=file\&file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1629192.bam samtools sort -n GSM1.2.5-dev9.bam > GSM1.2.5-dev9.qsort samtools sort -n GSM1629192.bam > GSM1629192.qsort samtools view GSM1.2.5-dev9.qsort HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.qsort2 samtools view GSM1629192.qsort HUMAN_21:9825832-48085036 > GSM1629192.qsort2 samtools sort -O BAM GSM1.2.5-dev9.bam > GSM1.2.5-dev9.sort.bam samtools sort -O BAM GSM1629192.bam > GSM1629192.sort.bam samtools index GSM1.2.5-dev9.sort.bam samtools index GSM1629192.sort.bam samtools view GSM1.2.5-dev9.sort.bam HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.chr21.bam samtools view GSM1629192.sort.bam HUMAN_21:9825832-48085036 > GSM1629192.chr21.bam samtools view -O BAM GSM1.2.5-dev9.sort.bam HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.chr21.sort.bam samtools view -O BAM GSM1629192.sort.bam HUMAN_21:9825832-48085036 > GSM1629192.chr21.sort.bam samtools sort -n GSM1.2.5-dev9.chr21.sort.bam -o GSM1.2.5-dev9.chr21.qsort.bam samtools sort -n GSM1629192.chr21.sort.bam -o GSM1629192.chr21.qsort.bam bedtools bamtofastq -i GSM1.2.5-dev9.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq bedtools bamtofastq -i GSM1629192.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq mv GSM1629193_chr21_R1.fastq GSM1629193_chr21_R2.fastq mv GSM1629193_chr21_R1.fastq GSM1629193_chr21_R2.fastq fastq-dump -F --split-files SRR1873277 fastq-dump -F --split-files SRR1873277 fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq Loading
