Loading test/shared/smartseq3-test/prepare_files.sh +39 −37 Original line number Diff line number Diff line wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-8735/Smartseq3.Fibroblasts.GelCut.R1.fastq.gz wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-8735/Smartseq3.Fibroblasts.GelCut.R2.fastq.gz wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-8735/Smartseq3.Fibroblasts.GelCut.I1.fastq.gz wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-8735/Smartseq3.Fibroblasts.GelCut.I2.fastq.gz rename "s/Smartseq3.Fibroblasts.GelCut./Smartseq3_Fibroblasts_GelCut_/g" Smartseq3.Fibroblasts.GelCut.*fastq.gz wget ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-8735/Smartseq3.diySpike.R1.fastq.gz . wget ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-8735/Smartseq3.diySpike.R2.fastq.gz . wget ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-8735/Smartseq3.diySpike.I1.fastq.gz . wget ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-8735/Smartseq3.diySpike.I2.fastq.gz . rename "s/.fastq/_001.fastq/g" Smartseq3_diySpike_S1*gz rename "s/.diySpike./_diySpike_S1_L001_/g" *gz #create bowtie index bowtie2-build ../../test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome.fa ../../test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome bowtie2 -x ../../test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome -U Smartseq3_Fibroblasts_GelCut_R2_001.fastq -S Smartseq3_Fibroblasts_GelCut_R2_001.sam samtools view -bS Smartseq3_Fibroblasts_GelCut_R2_001.sam > Smartseq3_Fibroblasts_GelCut_R2_001.bam bowtie2 -x ../../test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome -U Smartseq3_diySpike_S1_L001_R2_001.001.fastq -S Smartseq3_diySpike_S1_L001_R2_001.001.sam samtools view -bS Smartseq3_diySpike_S1_L001_R2_001.001.sam > Smartseq3_diySpike_S1_L001_R2_001.001.bam # extract region of genome samtools sort -O BAM Smartseq3_Fibroblasts_GelCut_R2_001.bam > Smartseq3_Fibroblasts_GelCut_R2_001.sort.bam samtools index Smartseq3_Fibroblasts_GelCut_R2_001.sort.bam samtools view Smartseq3_Fibroblasts_GelCut_R2_001.sort.bam 21:9825832-48085036 > Smartseq3_Fibroblasts_GelCut_R2_001.chr21.bam samtools view -O BAM Smartseq3_Fibroblasts_GelCut_R2_001.sort.bam 21:9825832-48085036 > Smartseq3_Fibroblasts_GelCut_R2_001.chr21.sort.bam samtools sort -n Smartseq3_Fibroblasts_GelCut_R2_001.chr21.sort.bam -o Smartseq3_Fibroblasts_GelCut_R2_001.chr21.qsort.bam samtools sort -O BAM Smartseq3_diySpike_S1_L001_R2_001.001.bam > Smartseq3_diySpike_S1_L001_R2_001.001.sort.bam samtools index Smartseq3_diySpike_S1_L001_R2_001.001.sort.bam samtools view Smartseq3_diySpike_S1_L001_R2_001.001.sort.bam 21:9825832-48085036 > Smartseq3_diySpike_S1_L001_R2_001.001.chr21.bam samtools view -O BAM Smartseq3_diySpike_S1_L001_R2_001.001.sort.bam 21:9825832-48085036 > Smartseq3_diySpike_S1_L001_R2_001.001.chr21.sort.bam samtools sort -n Smartseq3_diySpike_S1_L001_R2_001.001.chr21.sort.bam -o Smartseq3_diySpike_S1_L001_R2_001.001.chr21.qsort.bam # export mapped regions to fastq bedtools bamtofastq -i Smartseq3_Fibroblasts_GelCut_R2_001.chr21.qsort.bam -fq Smartseq3_Fibroblasts_GelCut_R2_001.chr21_R2.fastq fastq_pair Smartseq3_Fibroblasts_GelCut_R2_001.chr21_R2.fastq Smartseq3_Fibroblasts_GelCut_R1_001.fastq fastq_pair Smartseq3_Fibroblasts_GelCut_R2_001.chr21_R2.fastq Smartseq3_Fibroblasts_GelCut_I1_001.fastq fastq_pair Smartseq3_Fibroblasts_GelCut_R2_001.chr21_R2.fastq Smartseq3_Fibroblasts_GelCut_I2_001.fastq bedtools bamtofastq -i Smartseq3_diySpike_S1_L001_R2_001.001.chr21.qsort.bam -fq Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq fastq_pair Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq Smartseq3_diySpike_S1_L001_R1_001.fastq fastq_pair Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq Smartseq3_diySpike_S1_L001_I1_001.001.fastq fastq_pair Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq Smartseq3_diySpike_S1_L001_I2_001.001.fastq # downsample to 250,000 reads per "lane" seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_R1_001.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L001_R1_001.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_R2_001.chr21_R2.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L001_R2_001.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_I1_001.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L001_I1_001.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_I2_001.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L001_I2_001.fastq seqtk sample -s100 Smartseq3_Fibroblasts_GelCut_R1_001.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L002_R1_001.fastq seqtk sample -s100 Smartseq3_Fibroblasts_GelCut_R2_001.chr21_R2.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L002_R2_001.fastq seqtk sample -s100 Smartseq3_Fibroblasts_GelCut_I1_001.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L001_I1_001.fastq seqtk sample -s100 Smartseq3_Fibroblasts_GelCut_I2_001.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L001_I2_001.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_R1_001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_R1_001.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_R2_001.001.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_I1_001.001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_I1_001.001.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_I2_001.001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_I2_001.001.fastq seqtk sample -s100 Smartseq3_diySpike_S1_L001_R1_001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L002_R1_001.fastq seqtk sample -s100 Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L002_R2_001.fastq seqtk sample -s100 Smartseq3_diySpike_S1_L001_I1_001.001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_I1_001.001.fastq seqtk sample -s100 Smartseq3_diySpike_S1_L001_I2_001.001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_I2_001.001.fastq #subsample smaller files for testing rename "s/Smartseq3.Fibroblasts.GelCut./Smartseq3_Fibroblasts_GelCut_/g" Smartseq3.Fibroblasts.GelCut.*fastq* rename "s/Smartseq3_diySpike_S1_L001_/Smartseq3_diySpike_S1_L001_/g" Smartseq3_diySpike_S1_L001_*fastq* # subsample to 500,000 reads zcat Smartseq3_Fibroblasts_GelCut_R1.fastq.gz | head -n 2000000 > Smartseq3_Fibroblasts_GelCut_small_R1.fastq zcat Smartseq3_Fibroblasts_GelCut_R2.fastq.gz | head -n 2000000 > Smartseq3_Fibroblasts_GelCut_small_R2.fastq zcat Smartseq3_Fibroblasts_GelCut_I1.fastq.gz | head -n 2000000 > Smartseq3_Fibroblasts_GelCut_small_I1.fastq zcat Smartseq3_Fibroblasts_GelCut_I2.fastq.gz | head -n 2000000 > Smartseq3_Fibroblasts_GelCut_small_I2.fastq zcat Smartseq3_diySpike_S1_L001_R1_001.fastq.gz | head -n 2000000 > Smartseq3_diySpike_S1_L001_small_R1.fastq zcat Smartseq3_diySpike_S1_L001_R2_001.fastq.gz | head -n 2000000 > Smartseq3_diySpike_S1_L001_small_R2.fastq zcat Smartseq3_diySpike_S1_L001_I1_001.fastq.gz | head -n 2000000 > Smartseq3_diySpike_S1_L001_small_I1.fastq zcat Smartseq3_diySpike_S1_L001_I2_001.fastq.gz | head -n 2000000 > Smartseq3_diySpike_S1_L001_small_I2.fastq # subsample to 2.5 million reads seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_R1.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_med_R1.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_R2.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_med_R2.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_I1.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_med_I1.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_I2.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_med_I2.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_R1_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_med_R1.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_R2_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_med_R2.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_I1_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_med_I1.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_I2_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_med_I2.fastq # subsample to 25 million reads seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_R1.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_large_R1.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_R2.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_large_R2.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_I1.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_large_I1.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_I2.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_large_I2.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_R1_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_large_R1.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_R2_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_large_R2.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_I1_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_large_I1.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_I2_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_large_I2.fastq Loading
test/shared/smartseq3-test/prepare_files.sh +39 −37 Original line number Diff line number Diff line wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-8735/Smartseq3.Fibroblasts.GelCut.R1.fastq.gz wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-8735/Smartseq3.Fibroblasts.GelCut.R2.fastq.gz wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-8735/Smartseq3.Fibroblasts.GelCut.I1.fastq.gz wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-8735/Smartseq3.Fibroblasts.GelCut.I2.fastq.gz rename "s/Smartseq3.Fibroblasts.GelCut./Smartseq3_Fibroblasts_GelCut_/g" Smartseq3.Fibroblasts.GelCut.*fastq.gz wget ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-8735/Smartseq3.diySpike.R1.fastq.gz . wget ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-8735/Smartseq3.diySpike.R2.fastq.gz . wget ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-8735/Smartseq3.diySpike.I1.fastq.gz . wget ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-8735/Smartseq3.diySpike.I2.fastq.gz . rename "s/.fastq/_001.fastq/g" Smartseq3_diySpike_S1*gz rename "s/.diySpike./_diySpike_S1_L001_/g" *gz #create bowtie index bowtie2-build ../../test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome.fa ../../test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome bowtie2 -x ../../test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome -U Smartseq3_Fibroblasts_GelCut_R2_001.fastq -S Smartseq3_Fibroblasts_GelCut_R2_001.sam samtools view -bS Smartseq3_Fibroblasts_GelCut_R2_001.sam > Smartseq3_Fibroblasts_GelCut_R2_001.bam bowtie2 -x ../../test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome -U Smartseq3_diySpike_S1_L001_R2_001.001.fastq -S Smartseq3_diySpike_S1_L001_R2_001.001.sam samtools view -bS Smartseq3_diySpike_S1_L001_R2_001.001.sam > Smartseq3_diySpike_S1_L001_R2_001.001.bam # extract region of genome samtools sort -O BAM Smartseq3_Fibroblasts_GelCut_R2_001.bam > Smartseq3_Fibroblasts_GelCut_R2_001.sort.bam samtools index Smartseq3_Fibroblasts_GelCut_R2_001.sort.bam samtools view Smartseq3_Fibroblasts_GelCut_R2_001.sort.bam 21:9825832-48085036 > Smartseq3_Fibroblasts_GelCut_R2_001.chr21.bam samtools view -O BAM Smartseq3_Fibroblasts_GelCut_R2_001.sort.bam 21:9825832-48085036 > Smartseq3_Fibroblasts_GelCut_R2_001.chr21.sort.bam samtools sort -n Smartseq3_Fibroblasts_GelCut_R2_001.chr21.sort.bam -o Smartseq3_Fibroblasts_GelCut_R2_001.chr21.qsort.bam samtools sort -O BAM Smartseq3_diySpike_S1_L001_R2_001.001.bam > Smartseq3_diySpike_S1_L001_R2_001.001.sort.bam samtools index Smartseq3_diySpike_S1_L001_R2_001.001.sort.bam samtools view Smartseq3_diySpike_S1_L001_R2_001.001.sort.bam 21:9825832-48085036 > Smartseq3_diySpike_S1_L001_R2_001.001.chr21.bam samtools view -O BAM Smartseq3_diySpike_S1_L001_R2_001.001.sort.bam 21:9825832-48085036 > Smartseq3_diySpike_S1_L001_R2_001.001.chr21.sort.bam samtools sort -n Smartseq3_diySpike_S1_L001_R2_001.001.chr21.sort.bam -o Smartseq3_diySpike_S1_L001_R2_001.001.chr21.qsort.bam # export mapped regions to fastq bedtools bamtofastq -i Smartseq3_Fibroblasts_GelCut_R2_001.chr21.qsort.bam -fq Smartseq3_Fibroblasts_GelCut_R2_001.chr21_R2.fastq fastq_pair Smartseq3_Fibroblasts_GelCut_R2_001.chr21_R2.fastq Smartseq3_Fibroblasts_GelCut_R1_001.fastq fastq_pair Smartseq3_Fibroblasts_GelCut_R2_001.chr21_R2.fastq Smartseq3_Fibroblasts_GelCut_I1_001.fastq fastq_pair Smartseq3_Fibroblasts_GelCut_R2_001.chr21_R2.fastq Smartseq3_Fibroblasts_GelCut_I2_001.fastq bedtools bamtofastq -i Smartseq3_diySpike_S1_L001_R2_001.001.chr21.qsort.bam -fq Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq fastq_pair Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq Smartseq3_diySpike_S1_L001_R1_001.fastq fastq_pair Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq Smartseq3_diySpike_S1_L001_I1_001.001.fastq fastq_pair Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq Smartseq3_diySpike_S1_L001_I2_001.001.fastq # downsample to 250,000 reads per "lane" seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_R1_001.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L001_R1_001.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_R2_001.chr21_R2.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L001_R2_001.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_I1_001.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L001_I1_001.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_I2_001.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L001_I2_001.fastq seqtk sample -s100 Smartseq3_Fibroblasts_GelCut_R1_001.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L002_R1_001.fastq seqtk sample -s100 Smartseq3_Fibroblasts_GelCut_R2_001.chr21_R2.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L002_R2_001.fastq seqtk sample -s100 Smartseq3_Fibroblasts_GelCut_I1_001.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L001_I1_001.fastq seqtk sample -s100 Smartseq3_Fibroblasts_GelCut_I2_001.fastq.paired.fq 250000 > Smartseq3_Fibroblasts_GelCut_L001_I2_001.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_R1_001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_R1_001.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_R2_001.001.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_I1_001.001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_I1_001.001.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_I2_001.001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_I2_001.001.fastq seqtk sample -s100 Smartseq3_diySpike_S1_L001_R1_001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L002_R1_001.fastq seqtk sample -s100 Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L002_R2_001.fastq seqtk sample -s100 Smartseq3_diySpike_S1_L001_I1_001.001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_I1_001.001.fastq seqtk sample -s100 Smartseq3_diySpike_S1_L001_I2_001.001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_I2_001.001.fastq #subsample smaller files for testing rename "s/Smartseq3.Fibroblasts.GelCut./Smartseq3_Fibroblasts_GelCut_/g" Smartseq3.Fibroblasts.GelCut.*fastq* rename "s/Smartseq3_diySpike_S1_L001_/Smartseq3_diySpike_S1_L001_/g" Smartseq3_diySpike_S1_L001_*fastq* # subsample to 500,000 reads zcat Smartseq3_Fibroblasts_GelCut_R1.fastq.gz | head -n 2000000 > Smartseq3_Fibroblasts_GelCut_small_R1.fastq zcat Smartseq3_Fibroblasts_GelCut_R2.fastq.gz | head -n 2000000 > Smartseq3_Fibroblasts_GelCut_small_R2.fastq zcat Smartseq3_Fibroblasts_GelCut_I1.fastq.gz | head -n 2000000 > Smartseq3_Fibroblasts_GelCut_small_I1.fastq zcat Smartseq3_Fibroblasts_GelCut_I2.fastq.gz | head -n 2000000 > Smartseq3_Fibroblasts_GelCut_small_I2.fastq zcat Smartseq3_diySpike_S1_L001_R1_001.fastq.gz | head -n 2000000 > Smartseq3_diySpike_S1_L001_small_R1.fastq zcat Smartseq3_diySpike_S1_L001_R2_001.fastq.gz | head -n 2000000 > Smartseq3_diySpike_S1_L001_small_R2.fastq zcat Smartseq3_diySpike_S1_L001_I1_001.fastq.gz | head -n 2000000 > Smartseq3_diySpike_S1_L001_small_I1.fastq zcat Smartseq3_diySpike_S1_L001_I2_001.fastq.gz | head -n 2000000 > Smartseq3_diySpike_S1_L001_small_I2.fastq # subsample to 2.5 million reads seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_R1.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_med_R1.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_R2.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_med_R2.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_I1.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_med_I1.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_I2.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_med_I2.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_R1_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_med_R1.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_R2_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_med_R2.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_I1_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_med_I1.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_I2_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_med_I2.fastq # subsample to 25 million reads seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_R1.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_large_R1.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_R2.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_large_R2.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_I1.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_large_I1.fastq seqtk sample -s999 Smartseq3_Fibroblasts_GelCut_I2.fastq.gz 2500000 > Smartseq3_Fibroblasts_GelCut_large_I2.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_R1_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_large_R1.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_R2_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_large_R2.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_I1_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_large_I1.fastq seqtk sample -s999 Smartseq3_diySpike_S1_L001_I2_001.fastq.gz 2500000 > Smartseq3_diySpike_S1_L001_large_I2.fastq
