bzip2 -cd Cut_and_Run_CTCF_0_6million_20160315_PS_HsDm_CTCF_0_6-GSM2247138_1.fastq.bz2 | /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-GSM2247138.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_10million_20160315_PS_HsDm_CTCF_10-GSM2247140_1.fastq.bz2 | /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-GSM2247140.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_15min_20160401_PS_HsDm_CTCF_15-GSM2247147_1.fastq.bz2 | /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-GSM2247147.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_15s_20160628_PS_HsDm_CTCF_0602_B-GSM2433137_1.fastq.bz2 | /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-GSM2433137.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_1min_20160414_PS_HsDm_CTCF_1m-GSM2247142_1.fastq.bz2 | /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-GSM2247142.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_2_5million_20160315_PS_HsDm_CTCF_2_5-GSM2247139_1.fastq.bz2 | /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-GSM2247139.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_27min_20160628_PS_HsDm_CTCF_0602_F-GSM2433138_1.fastq.bz2 | /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-GSM2433138.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_2min_20160414_PS_HsDm_CTCF_2m-GSM2247143_1.fastq.bz2 | /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-GSM2247143.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_30min_20160401_PS_HsDm_CTCF_30-GSM2247148_1.fastq.bz2 | /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-GSM2247148.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_3min_20160628_PS_HsDm_CTCF_0602_D-GSM2433139_1.fastq.bz2 | /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-GSM2433139.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_45min_20160401_PS_HsDm_CTCF_45-GSM2247149_1.fastq.bz2 | /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-GSM2247149.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_45s_20160628_PS_HsDm_CTCF_0602_C-GSM2433140_1.fastq.bz2 | /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-GSM2433140.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_4min_20160414_PS_HsDm_CTCF_4m-GSM2247144_1.fastq.bz2 | /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-GSM2247144.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_5s_20160628_PS_HsDm_CTCF_0602_A-GSM2433141_1.fastq.bz2 | /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-GSM2433141.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_7_5min_20160401_PS_HsDm_CTCF_7_5-GSM2247145_1.fastq.bz2 | /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-GSM2247145.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_8min_20160414_PS_HsDm_CTCF_8m-GSM2247146_1.fastq.bz2 | /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-GSM2247146.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_9min_20160628_PS_HsDm_CTCF_0602_E-GSM2433142_1.fastq.bz2 | /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-GSM2433142.1x25mers.unique
bzip2 -cd Cut_and_Run_CTCF_disrupted_20160315_PS_HsDm_CTCF_expl_UB-GSM2247141_1.fastq.bz2 | /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-GSM2247141.1x25mers.unique
bzip2 -cd Cut_and_Run_no_antibody_size_selected_20161206_PS_HsDm_neg_30_1201-GSM2433147_1.fastq.bz2 | /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-GSM2433147.1x25mers.unique
bzip2 -cd Native_ChIP_CTCF_high_MNase_1_20150925_PS_Hs_N_CTCF_C-GSM2247154_1.fastq.bz2 | /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-GSM2247154.1x25mers.unique
bzip2 -cd Native_ChIP_CTCF_high_MNase_2_20151104_PS_Hs_N_CTCF_C-GSM2247155_1.fastq.bz2 | /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-GSM2247155.1x25mers.unique
bzip2 -cd Native_ChIP_CTCF_low_MNase_1_20150925_PS_Hs_N_CTCF_E-GSM2247150_1.fastq.bz2 | /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-GSM2247150.1x25mers.unique
bzip2 -cd Native_ChIP_CTCF_low_MNase_2_20151104_PS_Hs_N_CTCF_E-GSM2247151_1.fastq.bz2 | /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-GSM2247151.1x25mers.unique
bzip2 -cd Native_ChIP_CTCF_medium_MNase_1_20150925_PS_Hs_N_CTCF_D-GSM2247152_1.fastq.bz2 | /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-GSM2247152.1x25mers.unique
bzip2 -cd Native_ChIP_CTCF_medium_MNase_2_20151104_PS_Hs_N_CTCF_D-GSM2247153_1.fastq.bz2 | /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-GSM2247153.1x25mers.unique
bzip2 -cd Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158_1.fastq.bz2 | /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-GSM2247158.1x25mers.unique
bzip2 -cd Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156_1.fastq.bz2 | /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-GSM2247156.1x25mers.unique
bzip2 -cd Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157_1.fastq.bz2 | /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-GSM2247157.1x25mers.unique