python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_0_6million_20160315_PS_HsDm_CTCF_0_6-GSM2247138/SRR3933720_1.fastq.gz Cut_and_Run_CTCF_0_6million_20160315_PS_HsDm_CTCF_0_6-GSM2247138/SRR3933720_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR3933720.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_10million_20160315_PS_HsDm_CTCF_10-GSM2247140/SRR3933722_1.fastq.gz Cut_and_Run_CTCF_10million_20160315_PS_HsDm_CTCF_10-GSM2247140/SRR3933722_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_10million_20160315_PS_HsDm_CTCF_10-GSM2247140/SRR3933722.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_15min_20160401_PS_HsDm_CTCF_15-GSM2247147/SRR3933729_1.fastq.gz Cut_and_Run_CTCF_15min_20160401_PS_HsDm_CTCF_15-GSM2247147/SRR3933729_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_15min_20160401_PS_HsDm_CTCF_15-GSM2247147/SRR3933729.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_15s_20160628_PS_HsDm_CTCF_0602_B-GSM2433137/SRR5121036_1.fastq.gz Cut_and_Run_CTCF_15s_20160628_PS_HsDm_CTCF_0602_B-GSM2433137/SRR5121036_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR5121036.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_1min_20160414_PS_HsDm_CTCF_1m-GSM2247142/SRR3933724_1.fastq.gz Cut_and_Run_CTCF_1min_20160414_PS_HsDm_CTCF_1m-GSM2247142/SRR3933724_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_1min_20160414_PS_HsDm_CTCF_1m-GSM2247142/SRR3933724.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_2_5million_20160315_PS_HsDm_CTCF_2_5-GSM2247139/SRR3933721_1.fastq.gz Cut_and_Run_CTCF_2_5million_20160315_PS_HsDm_CTCF_2_5-GSM2247139/SRR3933721_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR3933721.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_27min_20160628_PS_HsDm_CTCF_0602_F-GSM2433138/SRR5121037_1.fastq.gz Cut_and_Run_CTCF_27min_20160628_PS_HsDm_CTCF_0602_F-GSM2433138/SRR5121037_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR5121037.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_2min_20160414_PS_HsDm_CTCF_2m-GSM2247143/SRR3933725_1.fastq.gz Cut_and_Run_CTCF_2min_20160414_PS_HsDm_CTCF_2m-GSM2247143/SRR3933725_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_2min_20160414_PS_HsDm_CTCF_2m-GSM2247143/SRR3933725.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_30min_20160401_PS_HsDm_CTCF_30-GSM2247148/SRR3933730_1.fastq.gz Cut_and_Run_CTCF_30min_20160401_PS_HsDm_CTCF_30-GSM2247148/SRR3933730_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_30min_20160401_PS_HsDm_CTCF_30-GSM2247148/SRR3933730.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_3min_20160628_PS_HsDm_CTCF_0602_D-GSM2433139/SRR5121038_1.fastq.gz Cut_and_Run_CTCF_3min_20160628_PS_HsDm_CTCF_0602_D-GSM2433139/SRR5121038_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR5121038.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_45min_20160401_PS_HsDm_CTCF_45-GSM2247149/SRR3933731_1.fastq.gz Cut_and_Run_CTCF_45min_20160401_PS_HsDm_CTCF_45-GSM2247149/SRR3933731_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_45min_20160401_PS_HsDm_CTCF_45-GSM2247149/SRR3933731.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_45s_20160628_PS_HsDm_CTCF_0602_C-GSM2433140/SRR5121039_1.fastq.gz Cut_and_Run_CTCF_45s_20160628_PS_HsDm_CTCF_0602_C-GSM2433140/SRR5121039_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR5121039.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_4min_20160414_PS_HsDm_CTCF_4m-GSM2247144/SRR3933726_1.fastq.gz Cut_and_Run_CTCF_4min_20160414_PS_HsDm_CTCF_4m-GSM2247144/SRR3933726_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_4min_20160414_PS_HsDm_CTCF_4m-GSM2247144/SRR3933726.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_5s_20160628_PS_HsDm_CTCF_0602_A-GSM2433141/SRR5121040_1.fastq.gz Cut_and_Run_CTCF_5s_20160628_PS_HsDm_CTCF_0602_A-GSM2433141/SRR5121040_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR5121040.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_7_5min_20160401_PS_HsDm_CTCF_7_5-GSM2247145/SRR3933727_1.fastq.gz Cut_and_Run_CTCF_7_5min_20160401_PS_HsDm_CTCF_7_5-GSM2247145/SRR3933727_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR3933727.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_8min_20160414_PS_HsDm_CTCF_8m-GSM2247146/SRR3933728_1.fastq.gz Cut_and_Run_CTCF_8min_20160414_PS_HsDm_CTCF_8m-GSM2247146/SRR3933728_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_CTCF_8min_20160414_PS_HsDm_CTCF_8m-GSM2247146/SRR3933728.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_9min_20160628_PS_HsDm_CTCF_0602_E-GSM2433142/SRR5121041_1.fastq.gz Cut_and_Run_CTCF_9min_20160628_PS_HsDm_CTCF_0602_E-GSM2433142/SRR5121041_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR5121041.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_CTCF_disrupted_20160315_PS_HsDm_CTCF_expl_UB-GSM2247141/SRR3933723_1.fastq.gz Cut_and_Run_CTCF_disrupted_20160315_PS_HsDm_CTCF_expl_UB-GSM2247141/SRR3933723_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR3933723.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_H3K27me3_liberated_20161206_PS_HsDm_H30_npc1121-GSM2433143/SRR5121042_1.fastq.gz Cut_and_Run_H3K27me3_liberated_20161206_PS_HsDm_H30_npc1121-GSM2433143/SRR5121042_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_H3K27me3_liberated_20161206_PS_HsDm_H30_npc1121-GSM2433143/SRR5121042.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_H3K27me3_size_selected_20161206_PS_HsDm_H30ss1121-GSM2433144/SRR5121043_1.fastq.gz Cut_and_Run_H3K27me3_size_selected_20161206_PS_HsDm_H30ss1121-GSM2433144/SRR5121043_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_H3K27me3_size_selected_20161206_PS_HsDm_H30ss1121-GSM2433144/SRR5121043.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_Max_size_selected_20161206_PS_HsDm_Max_30_1201-GSM2433145/SRR5121044_1.fastq.gz Cut_and_Run_Max_size_selected_20161206_PS_HsDm_Max_30_1201-GSM2433145/SRR5121044_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_Max_size_selected_20161206_PS_HsDm_Max_30_1201-GSM2433145/SRR5121044.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_Myc_size_selected_20161206_PS_HsDm_Myc_30_1201-GSM2433146/SRR5121045_1.fastq.gz Cut_and_Run_Myc_size_selected_20161206_PS_HsDm_Myc_30_1201-GSM2433146/SRR5121045_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut_and_Run_Myc_size_selected_20161206_PS_HsDm_Myc_30_1201-GSM2433146/SRR5121045.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut_and_Run_no_antibody_size_selected_20161206_PS_HsDm_neg_30_1201-GSM2433147/SRR5121046_1.fastq.gz Cut_and_Run_no_antibody_size_selected_20161206_PS_HsDm_neg_30_1201-GSM2433147/SRR5121046_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR5121046.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Native_ChIP_CTCF_high_MNase_1_20150925_PS_Hs_N_CTCF_C-GSM2247154/SRR3933736_1.fastq.gz Native_ChIP_CTCF_high_MNase_1_20150925_PS_Hs_N_CTCF_C-GSM2247154/SRR3933736_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR3933736.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Native_ChIP_CTCF_high_MNase_2_20151104_PS_Hs_N_CTCF_C-GSM2247155/SRR3933737_1.fastq.gz Native_ChIP_CTCF_high_MNase_2_20151104_PS_Hs_N_CTCF_C-GSM2247155/SRR3933737_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR3933737.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Native_ChIP_CTCF_low_MNase_1_20150925_PS_Hs_N_CTCF_E-GSM2247150/SRR3933732_1.fastq.gz Native_ChIP_CTCF_low_MNase_1_20150925_PS_Hs_N_CTCF_E-GSM2247150/SRR3933732_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR3933732.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Native_ChIP_CTCF_low_MNase_2_20151104_PS_Hs_N_CTCF_E-GSM2247151/SRR3933733_1.fastq.gz Native_ChIP_CTCF_low_MNase_2_20151104_PS_Hs_N_CTCF_E-GSM2247151/SRR3933733_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR3933733.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Native_ChIP_CTCF_medium_MNase_1_20150925_PS_Hs_N_CTCF_D-GSM2247152/SRR3933734_1.fastq.gz Native_ChIP_CTCF_medium_MNase_1_20150925_PS_Hs_N_CTCF_D-GSM2247152/SRR3933734_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR3933734.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Native_ChIP_CTCF_medium_MNase_2_20151104_PS_Hs_N_CTCF_D-GSM2247153/SRR3933735_1.fastq.gz Native_ChIP_CTCF_medium_MNase_2_20151104_PS_Hs_N_CTCF_D-GSM2247153/SRR3933735_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.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/SRR3933735.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158/SRR3933740_1.fastq.gz Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158/SRR3933740_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158/SRR3933740.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156/SRR3933738_1.fastq.gz Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156/SRR3933738_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156/SRR3933738.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157/SRR3933739_1.fastq.gz Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157/SRR3933739_2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157/SRR3933739.2x25mers.hg19.unique