zcat L418D6D10ATACCL01.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 20 -e 200 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L418D6D10ATACCL01.trimmed.hg38.chrM
zcat L418D6D10ATACCL01.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38 -p 20 -e 200 -k 2 -m 1 -t --best --strata -q --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L418D6D10ATACCL01.trimmed.hg38.unique.nochrM
zcat L420D6D10ATACCL03.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 20 -e 200 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L420D6D10ATACCL03.trimmed.hg38.chrM
zcat L420D6D10ATACCL03.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38 -p 20 -e 200 -k 2 -m 1 -t --best --strata -q --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L420D6D10ATACCL03.trimmed.hg38.unique.nochrM
zcat L430D6D10ATACCL09.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 20 -e 200 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L430D6D10ATACCL09.trimmed.hg38.chrM
zcat L430D6D10ATACCL09.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38 -p 20 -e 200 -k 2 -m 1 -t --best --strata -q --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L430D6D10ATACCL09.trimmed.hg38.unique.nochrM
zcat L431D6D10ATACCL10.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 20 -e 200 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L431D6D10ATACCL10.trimmed.hg38.chrM
zcat L431D6D10ATACCL10.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38 -p 20 -e 200 -k 2 -m 1 -t --best --strata -q --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L431D6D10ATACCL10.trimmed.hg38.unique.nochrM
zcat L434D6D10ATACCL13.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 20 -e 200 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L434D6D10ATACCL13.trimmed.hg38.chrM
zcat L434D6D10ATACCL13.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38 -p 20 -e 200 -k 2 -m 1 -t --best --strata -q --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L434D6D10ATACCL13.trimmed.hg38.unique.nochrM
zcat L435D6D10ATACCL14.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 20 -e 200 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L435D6D10ATACCL14.trimmed.hg38.chrM
zcat L435D6D10ATACCL14.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38 -p 20 -e 200 -k 2 -m 1 -t --best --strata -q --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L435D6D10ATACCL14.trimmed.hg38.unique.nochrM