Loading test/shared/dropseq-test/README.md 0 → 100644 +23 −0 Original line number Diff line number Diff line ## Test data for Drop-Seq technique (Nadia settings) ### Beads supplied by ChemGenes (12bp barcode, 8pm UMI) Citation: Macosko et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 161(5):1202-1214. doi: 10.1016/j.cell.2015.05.002. ## Data source Fastqs (Read 1) SRA Archive: https://www.ncbi.nlm.nih.gov/sra/?term=SRR1873277 Bam files (Read2) Gene Expression Omnibus (GEO) Experiment Accession: GSE63473 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63473 Sample Accession: GSM1629192 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1629192 ## Data preparations Filtered for regions mapping to HUMAN_21:9825832-48085036 GRCh38 (hg38) f Matched by fastq_pair (https://github.com/linsalrob/fastq-pair) test/shared/dropseq-test/prepare_files.sh 0 → 100644 +20 −0 Original line number Diff line number Diff line wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1629192\&format\=file\&file\=GSM1629192%5FPure%5FHumanMouse%2Ebam mv index.html\?acc=GSM1629192\&format=file\&file=GSM1629192%5FPure%5FHumanMouse%2Ebam GSM162919.bam samtools sort -n GSM162919.bam > GSM162919.qsort samtools view GSM162919.qsort HUMAN_21:9825832-48085036 > GSM162919.qsort2 samtools sort -O BAM GSM162919.bam > GSM162919.sort.bam samtools index GSM162919.sort.bam samtools view GSM162919.sort.bam HUMAN_21:9825832-48085036 > GSM162919.chr21.bam samtools view -O BAM GSM162919.sort.bam HUMAN_21:9825832-48085036 > GSM162919.chr21.sort.bam samtools sort -n GSM162919.chr21.sort.bam -o GSM162919.chr21.qsort.bam bedtools bamtofastq -i GSM162919.chr21.qsort.bam -fq GSM1629192_chr21_R1.fastq mv GSM1629192_chr21_R1.fastq GSM1629192_chr21_R2.fastq fastq-dump -F --split-files SRR1873277 fastq_pair GSM1629192_chr21_R2.fastq SRR1873277_1.fastq head -n 117060 SRR1873277_1.fastq.paired.fq 117060 > SRR1873277_1.fastq.paired.fq head -n 117060 GSM1629192_chr21_R2.fastq.paired.fq > GSM1629192_chr21_R2.fastq.paired.fq cp SRR1873277_1.fastq.paired.fq GSM1629192_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test cp SRR1873277_1.fastq.paired.fq GSM1629192_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test mv SRR1873277_1.fastq.paired.fq SRR1873277_R1.fastq mv GSM1629192_chr21_R2.fastq.paired.fq SRR1873277_R2.fastq mv GSM1629192_chr21_R2.fastq.paired.fq SRR1873277_R2.fastq Loading
test/shared/dropseq-test/README.md 0 → 100644 +23 −0 Original line number Diff line number Diff line ## Test data for Drop-Seq technique (Nadia settings) ### Beads supplied by ChemGenes (12bp barcode, 8pm UMI) Citation: Macosko et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 161(5):1202-1214. doi: 10.1016/j.cell.2015.05.002. ## Data source Fastqs (Read 1) SRA Archive: https://www.ncbi.nlm.nih.gov/sra/?term=SRR1873277 Bam files (Read2) Gene Expression Omnibus (GEO) Experiment Accession: GSE63473 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63473 Sample Accession: GSM1629192 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1629192 ## Data preparations Filtered for regions mapping to HUMAN_21:9825832-48085036 GRCh38 (hg38) f Matched by fastq_pair (https://github.com/linsalrob/fastq-pair)
test/shared/dropseq-test/prepare_files.sh 0 → 100644 +20 −0 Original line number Diff line number Diff line wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1629192\&format\=file\&file\=GSM1629192%5FPure%5FHumanMouse%2Ebam mv index.html\?acc=GSM1629192\&format=file\&file=GSM1629192%5FPure%5FHumanMouse%2Ebam GSM162919.bam samtools sort -n GSM162919.bam > GSM162919.qsort samtools view GSM162919.qsort HUMAN_21:9825832-48085036 > GSM162919.qsort2 samtools sort -O BAM GSM162919.bam > GSM162919.sort.bam samtools index GSM162919.sort.bam samtools view GSM162919.sort.bam HUMAN_21:9825832-48085036 > GSM162919.chr21.bam samtools view -O BAM GSM162919.sort.bam HUMAN_21:9825832-48085036 > GSM162919.chr21.sort.bam samtools sort -n GSM162919.chr21.sort.bam -o GSM162919.chr21.qsort.bam bedtools bamtofastq -i GSM162919.chr21.qsort.bam -fq GSM1629192_chr21_R1.fastq mv GSM1629192_chr21_R1.fastq GSM1629192_chr21_R2.fastq fastq-dump -F --split-files SRR1873277 fastq_pair GSM1629192_chr21_R2.fastq SRR1873277_1.fastq head -n 117060 SRR1873277_1.fastq.paired.fq 117060 > SRR1873277_1.fastq.paired.fq head -n 117060 GSM1629192_chr21_R2.fastq.paired.fq > GSM1629192_chr21_R2.fastq.paired.fq cp SRR1873277_1.fastq.paired.fq GSM1629192_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test cp SRR1873277_1.fastq.paired.fq GSM1629192_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test mv SRR1873277_1.fastq.paired.fq SRR1873277_R1.fastq mv GSM1629192_chr21_R2.fastq.paired.fq SRR1873277_R2.fastq mv GSM1629192_chr21_R2.fastq.paired.fq SRR1873277_R2.fastq
