zcat 170858-BC01.barcodes_annotated.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 - 170858-BC01.trimmed.hg38.chrM
zcat 170858-BC02.barcodes_annotated.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 - 170858-BC02.trimmed.hg38.chrM
zcat 170858-BC03.barcodes_annotated.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 - 170858-BC03.trimmed.hg38.chrM
zcat 170858-BC04.barcodes_annotated.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 - 170858-BC04.trimmed.hg38.chrM
zcat 170858-BC05.barcodes_annotated.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 - 170858-BC05.trimmed.hg38.chrM
zcat 170858-BC06.barcodes_annotated.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 - 170858-BC06.trimmed.hg38.chrM
zcat 170858-BC07_8old.barcodes_annotated.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 - 170858-BC07_8old.trimmed.hg38.chrM
zcat 170858-BC08_9old.barcodes_annotated.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 - 170858-BC08_9old.trimmed.hg38.chrM
zcat 170858-BC10_9old.barcodes_annotated.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 - 170858-BC10_9old.trimmed.hg38.chrM
zcat 170858-BC11_10old.barcodes_annotated.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 - 170858-BC11_10old.trimmed.hg38.chrM
zcat 170858-BC12_11old.barcodes_annotated.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 - 170858-BC12_11old.trimmed.hg38.chrM
zcat 170858-BC13_12old.barcodes_annotated.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 - 170858-BC13_12old.trimmed.hg38.chrM
zcat 170858-BC14_13old.barcodes_annotated.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 - 170858-BC14_13old.trimmed.hg38.chrM
zcat 170858-BC15_14old.barcodes_annotated.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 - 170858-BC15_14old.trimmed.hg38.chrM
zcat 170858-BC16_15old.barcodes_annotated.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 - 170858-BC16_15old.trimmed.hg38.chrM
zcat 170858-BC17_16old.barcodes_annotated.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 - 170858-BC17_16old.trimmed.hg38.chrM
zcat 170858-BC18_17old.barcodes_annotated.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 - 170858-BC18_17old.trimmed.hg38.chrM
zcat 170858-BC19_18old.barcodes_annotated.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 - 170858-BC19_18old.trimmed.hg38.chrM
zcat 170858-BC20_19old.barcodes_annotated.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 - 170858-BC20_19old.trimmed.hg38.chrM
zcat 170858-BC23_20old.barcodes_annotated.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 - 170858-BC23_20old.trimmed.hg38.chrM
zcat 170858-BC24_21old.barcodes_annotated.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 - 170858-BC24_21old.trimmed.hg38.chrM
zcat 170858-BC26_22old.barcodes_annotated.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 - 170858-BC26_22old.trimmed.hg38.chrM
zcat 170858-BC27_23old.barcodes_annotated.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 - 170858-BC27_23old.trimmed.hg38.chrM
zcat 170858-BC28_24old.barcodes_annotated.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 - 170858-BC28_24old.trimmed.hg38.chrM
zcat 170858-BC29_25old.barcodes_annotated.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 - 170858-BC29_25old.trimmed.hg38.chrM
zcat 170858-BC30_26old.barcodes_annotated.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 - 170858-BC30_26old.trimmed.hg38.chrM
zcat 170858-BC31_27old.barcodes_annotated.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 - 170858-BC31_27old.trimmed.hg38.chrM
zcat 170858-BC32_28old.barcodes_annotated.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 - 170858-BC32_28old.trimmed.hg38.chrM
zcat 170858-BC33_29old.barcodes_annotated.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 - 170858-BC33_29old.trimmed.hg38.chrM
zcat 170858-BC34_30old.barcodes_annotated.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 - 170858-BC34_30old.trimmed.hg38.chrM
zcat 170858-BC01.barcodes_annotated.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 - 170858-BC01.trimmed.hg38.unique.nochrM
zcat 170858-BC02.barcodes_annotated.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 - 170858-BC02.trimmed.hg38.unique.nochrM
zcat 170858-BC03.barcodes_annotated.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 - 170858-BC03.trimmed.hg38.unique.nochrM
zcat 170858-BC04.barcodes_annotated.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 - 170858-BC04.trimmed.hg38.unique.nochrM
zcat 170858-BC05.barcodes_annotated.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 - 170858-BC05.trimmed.hg38.unique.nochrM
zcat 170858-BC06.barcodes_annotated.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 - 170858-BC06.trimmed.hg38.unique.nochrM
zcat 170858-BC07_8old.barcodes_annotated.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 - 170858-BC07_8old.trimmed.hg38.unique.nochrM
zcat 170858-BC08_9old.barcodes_annotated.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 - 170858-BC08_9old.trimmed.hg38.unique.nochrM
zcat 170858-BC10_9old.barcodes_annotated.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 - 170858-BC10_9old.trimmed.hg38.unique.nochrM
zcat 170858-BC11_10old.barcodes_annotated.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 - 170858-BC11_10old.trimmed.hg38.unique.nochrM
zcat 170858-BC12_11old.barcodes_annotated.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 - 170858-BC12_11old.trimmed.hg38.unique.nochrM
zcat 170858-BC13_12old.barcodes_annotated.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 - 170858-BC13_12old.trimmed.hg38.unique.nochrM
zcat 170858-BC14_13old.barcodes_annotated.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 - 170858-BC14_13old.trimmed.hg38.unique.nochrM
zcat 170858-BC15_14old.barcodes_annotated.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 - 170858-BC15_14old.trimmed.hg38.unique.nochrM
zcat 170858-BC16_15old.barcodes_annotated.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 - 170858-BC16_15old.trimmed.hg38.unique.nochrM
zcat 170858-BC17_16old.barcodes_annotated.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 - 170858-BC17_16old.trimmed.hg38.unique.nochrM
zcat 170858-BC18_17old.barcodes_annotated.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 - 170858-BC18_17old.trimmed.hg38.unique.nochrM
zcat 170858-BC19_18old.barcodes_annotated.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 - 170858-BC19_18old.trimmed.hg38.unique.nochrM
zcat 170858-BC20_19old.barcodes_annotated.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 - 170858-BC20_19old.trimmed.hg38.unique.nochrM
zcat 170858-BC23_20old.barcodes_annotated.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 - 170858-BC23_20old.trimmed.hg38.unique.nochrM
zcat 170858-BC24_21old.barcodes_annotated.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 - 170858-BC24_21old.trimmed.hg38.unique.nochrM
zcat 170858-BC26_22old.barcodes_annotated.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 - 170858-BC26_22old.trimmed.hg38.unique.nochrM
zcat 170858-BC27_23old.barcodes_annotated.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 - 170858-BC27_23old.trimmed.hg38.unique.nochrM
zcat 170858-BC28_24old.barcodes_annotated.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 - 170858-BC28_24old.trimmed.hg38.unique.nochrM
zcat 170858-BC29_25old.barcodes_annotated.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 - 170858-BC29_25old.trimmed.hg38.unique.nochrM
zcat 170858-BC30_26old.barcodes_annotated.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 - 170858-BC30_26old.trimmed.hg38.unique.nochrM
zcat 170858-BC31_27old.barcodes_annotated.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 - 170858-BC31_27old.trimmed.hg38.unique.nochrM
zcat 170858-BC32_28old.barcodes_annotated.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 - 170858-BC32_28old.trimmed.hg38.unique.nochrM
zcat 170858-BC33_29old.barcodes_annotated.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 - 170858-BC33_29old.trimmed.hg38.unique.nochrM
zcat 170858-BC34_30old.barcodes_annotated.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 - 170858-BC34_30old.trimmed.hg38.unique.nochrM