zcat Cut_and_Run_CTCF_0_6million_20160315_PS_HsDm_CTCF_0_6-GSM2247138.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_0_6million_20160315_PS_HsDm_CTCF_0_6-GSM2247138.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_0_6million_20160315_PS_HsDm_CTCF_0_6-GSM2247138.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_0_6million_20160315_PS_HsDm_CTCF_0_6-GSM2247138.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_10million_20160315_PS_HsDm_CTCF_10-GSM2247140.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_10million_20160315_PS_HsDm_CTCF_10-GSM2247140.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_10million_20160315_PS_HsDm_CTCF_10-GSM2247140.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_10million_20160315_PS_HsDm_CTCF_10-GSM2247140.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_15min_20160401_PS_HsDm_CTCF_15-GSM2247147.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_15min_20160401_PS_HsDm_CTCF_15-GSM2247147.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_15min_20160401_PS_HsDm_CTCF_15-GSM2247147.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_15min_20160401_PS_HsDm_CTCF_15-GSM2247147.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_15s_20160628_PS_HsDm_CTCF_0602_B-GSM2433137.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_15s_20160628_PS_HsDm_CTCF_0602_B-GSM2433137.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_15s_20160628_PS_HsDm_CTCF_0602_B-GSM2433137.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_15s_20160628_PS_HsDm_CTCF_0602_B-GSM2433137.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_1min_20160414_PS_HsDm_CTCF_1m-GSM2247142.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_1min_20160414_PS_HsDm_CTCF_1m-GSM2247142.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_1min_20160414_PS_HsDm_CTCF_1m-GSM2247142.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_1min_20160414_PS_HsDm_CTCF_1m-GSM2247142.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_2_5million_20160315_PS_HsDm_CTCF_2_5-GSM2247139.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_2_5million_20160315_PS_HsDm_CTCF_2_5-GSM2247139.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_2_5million_20160315_PS_HsDm_CTCF_2_5-GSM2247139.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_2_5million_20160315_PS_HsDm_CTCF_2_5-GSM2247139.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_27min_20160628_PS_HsDm_CTCF_0602_F-GSM2433138.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_27min_20160628_PS_HsDm_CTCF_0602_F-GSM2433138.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_27min_20160628_PS_HsDm_CTCF_0602_F-GSM2433138.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_27min_20160628_PS_HsDm_CTCF_0602_F-GSM2433138.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_2min_20160414_PS_HsDm_CTCF_2m-GSM2247143.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_2min_20160414_PS_HsDm_CTCF_2m-GSM2247143.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_2min_20160414_PS_HsDm_CTCF_2m-GSM2247143.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_2min_20160414_PS_HsDm_CTCF_2m-GSM2247143.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_30min_20160401_PS_HsDm_CTCF_30-GSM2247148.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_30min_20160401_PS_HsDm_CTCF_30-GSM2247148.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_30min_20160401_PS_HsDm_CTCF_30-GSM2247148.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_30min_20160401_PS_HsDm_CTCF_30-GSM2247148.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_3min_20160628_PS_HsDm_CTCF_0602_D-GSM2433139.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_3min_20160628_PS_HsDm_CTCF_0602_D-GSM2433139.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_3min_20160628_PS_HsDm_CTCF_0602_D-GSM2433139.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_3min_20160628_PS_HsDm_CTCF_0602_D-GSM2433139.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_45min_20160401_PS_HsDm_CTCF_45-GSM2247149.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_45min_20160401_PS_HsDm_CTCF_45-GSM2247149.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_45min_20160401_PS_HsDm_CTCF_45-GSM2247149.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_45min_20160401_PS_HsDm_CTCF_45-GSM2247149.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_45s_20160628_PS_HsDm_CTCF_0602_C-GSM2433140.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_45s_20160628_PS_HsDm_CTCF_0602_C-GSM2433140.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_45s_20160628_PS_HsDm_CTCF_0602_C-GSM2433140.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_45s_20160628_PS_HsDm_CTCF_0602_C-GSM2433140.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_4min_20160414_PS_HsDm_CTCF_4m-GSM2247144.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_4min_20160414_PS_HsDm_CTCF_4m-GSM2247144.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_4min_20160414_PS_HsDm_CTCF_4m-GSM2247144.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_4min_20160414_PS_HsDm_CTCF_4m-GSM2247144.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_5s_20160628_PS_HsDm_CTCF_0602_A-GSM2433141.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_5s_20160628_PS_HsDm_CTCF_0602_A-GSM2433141.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_5s_20160628_PS_HsDm_CTCF_0602_A-GSM2433141.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_5s_20160628_PS_HsDm_CTCF_0602_A-GSM2433141.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_7_5min_20160401_PS_HsDm_CTCF_7_5-GSM2247145.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_7_5min_20160401_PS_HsDm_CTCF_7_5-GSM2247145.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_7_5min_20160401_PS_HsDm_CTCF_7_5-GSM2247145.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_7_5min_20160401_PS_HsDm_CTCF_7_5-GSM2247145.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_8min_20160414_PS_HsDm_CTCF_8m-GSM2247146.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_8min_20160414_PS_HsDm_CTCF_8m-GSM2247146.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_8min_20160414_PS_HsDm_CTCF_8m-GSM2247146.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_8min_20160414_PS_HsDm_CTCF_8m-GSM2247146.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_9min_20160628_PS_HsDm_CTCF_0602_E-GSM2433142.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_9min_20160628_PS_HsDm_CTCF_0602_E-GSM2433142.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_9min_20160628_PS_HsDm_CTCF_0602_E-GSM2433142.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_9min_20160628_PS_HsDm_CTCF_0602_E-GSM2433142.minFL150bp.1x25mers.unique
zcat Cut_and_Run_CTCF_disrupted_20160315_PS_HsDm_CTCF_expl_UB-GSM2247141.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_disrupted_20160315_PS_HsDm_CTCF_expl_UB-GSM2247141.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_CTCF_disrupted_20160315_PS_HsDm_CTCF_expl_UB-GSM2247141.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_disrupted_20160315_PS_HsDm_CTCF_expl_UB-GSM2247141.minFL150bp.1x25mers.unique
zcat Cut_and_Run_no_antibody_size_selected_20161206_PS_HsDm_neg_30_1201-GSM2433147.2x25mers.unique.maxFL120bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_no_antibody_size_selected_20161206_PS_HsDm_neg_30_1201-GSM2433147.maxFL120bp.1x25mers.unique
zcat Cut_and_Run_no_antibody_size_selected_20161206_PS_HsDm_neg_30_1201-GSM2433147.2x25mers.unique.minFL150bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_no_antibody_size_selected_20161206_PS_HsDm_neg_30_1201-GSM2433147.minFL150bp.1x25mers.unique
zcat Native_ChIP_CTCF_high_MNase_1_20150925_PS_Hs_N_CTCF_C-GSM2247154.2x25mers.unique.FL20-75bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Native_ChIP_CTCF_high_MNase_1_20150925_PS_Hs_N_CTCF_C-GSM2247154.FL20-75bp.1x25mers.unique
zcat Native_ChIP_CTCF_high_MNase_2_20151104_PS_Hs_N_CTCF_C-GSM2247155.2x25mers.unique.FL20-75bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Native_ChIP_CTCF_high_MNase_2_20151104_PS_Hs_N_CTCF_C-GSM2247155.FL20-75bp.1x25mers.unique
zcat Native_ChIP_CTCF_low_MNase_1_20150925_PS_Hs_N_CTCF_E-GSM2247150.2x25mers.unique.FL20-75bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Native_ChIP_CTCF_low_MNase_1_20150925_PS_Hs_N_CTCF_E-GSM2247150.FL20-75bp.1x25mers.unique
zcat Native_ChIP_CTCF_low_MNase_2_20151104_PS_Hs_N_CTCF_E-GSM2247151.2x25mers.unique.FL20-75bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Native_ChIP_CTCF_low_MNase_2_20151104_PS_Hs_N_CTCF_E-GSM2247151.FL20-75bp.1x25mers.unique
zcat Native_ChIP_CTCF_medium_MNase_1_20150925_PS_Hs_N_CTCF_D-GSM2247152.2x25mers.unique.FL20-75bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Native_ChIP_CTCF_medium_MNase_1_20150925_PS_Hs_N_CTCF_D-GSM2247152.FL20-75bp.1x25mers.unique
zcat Native_ChIP_CTCF_medium_MNase_2_20151104_PS_Hs_N_CTCF_D-GSM2247153.2x25mers.unique.FL20-75bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Native_ChIP_CTCF_medium_MNase_2_20151104_PS_Hs_N_CTCF_D-GSM2247153.FL20-75bp.1x25mers.unique
zcat Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158.2x25mers.unique.FL20-75bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158.FL20-75bp.1x25mers.unique
zcat Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156.2x25mers.unique.FL20-75bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156.FL20-75bp.1x25mers.unique
zcat Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157.2x25mers.unique.FL20-75bp.end1.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157.FL20-75bp.1x25mers.unique