python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-10K-CGCTCATT-GCCTCTAT_S10_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-10K-CGCTCATT-GCCTCTAT_S10_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-CTCF-10K.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-250K-1-100Ab-TAATGCGC-AGGCTATA_S3_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-250K-1-100Ab-TAATGCGC-AGGCTATA_S3_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-CTCF-250K-1-100Ab.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-250K-1-200-ATTACTCG-GCCTCTAT_S8_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-250K-1-200-ATTACTCG-GCCTCTAT_S8_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-CTCF-250K-1-200.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-250K-1-20Ab-TCCGGAGA-AGGCTATA_S1_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-250K-1-20Ab-TCCGGAGA-AGGCTATA_S1_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-CTCF-250K-1-20Ab.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-250K-15-min-CGGCTATG-AGGCTATA_S4_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-250K-15-min-CGGCTATG-AGGCTATA_S4_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-CTCF-250K-15-min.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-250K-30min-TCCGGAGA-GCCTCTAT_S9_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-250K-30min-TCCGGAGA-GCCTCTAT_S9_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-CTCF-250K-30min.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-250K-5-min-CGCTCATT-AGGCTATA_S2_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-250K-5-min-CGCTCATT-AGGCTATA_S2_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-CTCF-250K-5-min.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-250K-CGGCTATG-GCCTCTAT_S16_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-250K-CGGCTATG-GCCTCTAT_S16_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-CTCF-250K.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-50K-GAATTCGT-GCCTCTAT_S13_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-50K-GAATTCGT-GCCTCTAT_S13_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-CTCF-50K.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-5K-TCCGCGAA-AGGCTATA_S5_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/CTCF-5K-TCCGCGAA-AGGCTATA_S5_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-CTCF-5K.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K27ac-10K-ATTCAGAA-GCCTCTAT_S12_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K27ac-10K-ATTCAGAA-GCCTCTAT_S12_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-H3K27ac-10K.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K27ac-250K-TCTCGCGC-GCCTCTAT_S18_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K27ac-250K-TCTCGCGC-GCCTCTAT_S18_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-H3K27ac-250K.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K27ac-50K-TAATGCGC-GCCTCTAT_S15_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K27ac-50K-TAATGCGC-GCCTCTAT_S15_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-H3K27ac-50K.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K27ac-5K-AGCGATAG-AGGCTATA_S7_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K27ac-5K-AGCGATAG-AGGCTATA_S7_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-H3K27ac-5K.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K4me1-10K-GAGATTCC-GCCTCTAT_S11_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K4me1-10K-GAGATTCC-GCCTCTAT_S11_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-H3K4me1-10K.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K4me1-250K-TCCGCGAA-GCCTCTAT_S17_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K4me1-250K-TCCGCGAA-GCCTCTAT_S17_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-H3K4me1-250K.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K4me1-50K-CTGAAGCT-GCCTCTAT_S14_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K4me1-50K-CTGAAGCT-GCCTCTAT_S14_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-H3K4me1-50K.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K4me1-5K-TCTCGCGC-AGGCTATA_S6_R1_001.fastq /oak/stanford/groups/wjg/seqruns/07182018_Arwa_Amy_plateCutNRun/180710_NS500615_0730_AH3JTHBGX7/K4me1-5K-TCTCGCGC-AGGCTATA_S6_R2_001.fastq -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 - 2018-07-18_Arwa_Amy_plateCutNRun-H3K4me1-5K.2x25mers.hg19.unique