python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/ac27_250k_neb_S2_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/ac27_250k_neb_S2_R2_001.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 - 2018-09-28-plateCUTnRUNtest-H3K27ac_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/Amy_K27ac-1-10-10m_S35_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/Amy_K27ac-1-10-10m_S35_R2_001.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 - 2018-09-28-plateCUTnRUNtest-Amy_K27ac-1-10-10m.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/Amy_K27ac-1-25-20m_S36_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/Amy_K27ac-1-25-20m_S36_R2_001.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 - 2018-09-28-plateCUTnRUNtest-Amy_K27ac-1-25-20m.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/Amy_K27ac-1-25-30m_S38_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/Amy_K27ac-1-25-30m_S38_R2_001.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 - 2018-09-28-plateCUTnRUNtest-Amy_K27ac-1-25-30m.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/Amy_K27ac-1-50-20m_S37_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/Amy_K27ac-1-50-20m_S37_R2_001.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 - 2018-09-28-plateCUTnRUNtest-Amy_K27ac-1-50-20m.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/Amy_K27ac-1-50-30m_S39_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/Amy_K27ac-1-50-30m_S39_R2_001.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 - 2018-09-28-plateCUTnRUNtest-Amy_K27ac-1-50-30m.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/Amy_K4me1_S34_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/Amy_K4me1_S34_R2_001.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 - 2018-09-28-plateCUTnRUNtest-Amy_K4me1_S34.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/atf3_1_100_250k_neb_S6_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/atf3_1_100_250k_neb_S6_R2_001.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 - 2018-09-28-plateCUTnRUNtest-ATF3_1_100_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/atf3_1_100_50k_neb_S21_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/atf3_1_100_50k_neb_S21_R2_001.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 - 2018-09-28-plateCUTnRUNtest-ATF3_1_100_50k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/atf3_1_2500_250k_neb_S16_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/atf3_1_2500_250k_neb_S16_R2_001.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 - 2018-09-28-plateCUTnRUNtest-ATF3_1_2500_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/atf3_1_2500_50k_neb_S31_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/atf3_1_2500_50k_neb_S31_R2_001.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 - 2018-09-28-plateCUTnRUNtest-ATF3_1_2500_50k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/atf3_1_500_250k_neb_S11_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/atf3_1_500_250k_neb_S11_R2_001.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 - 2018-09-28-plateCUTnRUNtest-ATF3_1_500_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/atf3_1_500_50k_neb_S26_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/atf3_1_500_50k_neb_S26_R2_001.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 - 2018-09-28-plateCUTnRUNtest-ATF3_1_500_50k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/cohesin_1_100_250k_neb_S4_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/cohesin_1_100_250k_neb_S4_R2_001.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 - 2018-09-28-plateCUTnRUNtest-Cohesin_1_100_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/cohesin_1_100_50k_neb_S19_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/cohesin_1_100_50k_neb_S19_R2_001.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 - 2018-09-28-plateCUTnRUNtest-Cohesin_1_100_50k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/cohesin_1_2500_250k_neb_S14_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/cohesin_1_2500_250k_neb_S14_R2_001.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 - 2018-09-28-plateCUTnRUNtest-Cohesin_1_2500_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/cohesin_1_2500_50k_neb_S29_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/cohesin_1_2500_50k_neb_S29_R2_001.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 - 2018-09-28-plateCUTnRUNtest-Cohesin_1_2500_50k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/cohesin_1_500_250k_neb_S9_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/cohesin_1_500_250k_neb_S9_R2_001.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 - 2018-09-28-plateCUTnRUNtest-Cohesin_1_500_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/cohesin_1_500_50k_neb_S24_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/cohesin_1_500_50k_neb_S24_R2_001.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 - 2018-09-28-plateCUTnRUNtest-Cohesin_1_500_50k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/gata1_1_100_250k_neb_S5_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/gata1_1_100_250k_neb_S5_R2_001.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 - 2018-09-28-plateCUTnRUNtest-GATA1_1_100_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/gata1_1_100_50k_neb_S20_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/gata1_1_100_50k_neb_S20_R2_001.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 - 2018-09-28-plateCUTnRUNtest-GATA1_1_100_50k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/gata1_1_2500_250k_neb_S15_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/gata1_1_2500_250k_neb_S15_R2_001.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 - 2018-09-28-plateCUTnRUNtest-GATA1_1_2500_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/gata1_1_2500_50k_neb_S30_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/gata1_1_2500_50k_neb_S30_R2_001.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 - 2018-09-28-plateCUTnRUNtest-GATA1_1_2500_50k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/gata1_1_500_250k_neb_S10_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/gata1_1_500_250k_neb_S10_R2_001.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 - 2018-09-28-plateCUTnRUNtest-GATA1_1_500_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/gata1_1_500_50k_neb_S25_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/gata1_1_500_50k_neb_S25_R2_001.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 - 2018-09-28-plateCUTnRUNtest-GATA1_1_500_50k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/klf1_1_100_250k_neb_S7_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/klf1_1_100_250k_neb_S7_R2_001.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 - 2018-09-28-plateCUTnRUNtest-KLF1_1_100_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/klf1_1_100_50k_neb_S22_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/klf1_1_100_50k_neb_S22_R2_001.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 - 2018-09-28-plateCUTnRUNtest-KLF1_1_100_50k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/klf1_1_2500_250k_neb_S17_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/klf1_1_2500_250k_neb_S17_R2_001.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 - 2018-09-28-plateCUTnRUNtest-KLF1_1_2500_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/klf1_1_500_250k_neb_S12_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/klf1_1_500_250k_neb_S12_R2_001.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 - 2018-09-28-plateCUTnRUNtest-KLF1_1_500_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/klf1_1_500_50k_neb_S27_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/klf1_1_500_50k_neb_S27_R2_001.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 - 2018-09-28-plateCUTnRUNtest-KLF1_1_500_50k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/me1_250k_hm_S32_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/me1_250k_hm_S32_R2_001.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 - 2018-09-28-plateCUTnRUNtest-H3K4me1_250k_hm.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/me1_250k_neb_S1_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/me1_250k_neb_S1_R2_001.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 - 2018-09-28-plateCUTnRUNtest-H3K4me1_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/tal1_1_100_250k_neb_S3_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/tal1_1_100_250k_neb_S3_R2_001.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 - 2018-09-28-plateCUTnRUNtest-TAL1_1_100_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/tal1_1_100_50k_neb_S18_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/tal1_1_100_50k_neb_S18_R2_001.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 - 2018-09-28-plateCUTnRUNtest-TAL1_1_100_50k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/tal1_1_2500_250k_neb_S13_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/tal1_1_2500_250k_neb_S13_R2_001.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 - 2018-09-28-plateCUTnRUNtest-TAL1_1_2500_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/tal1_1_2500_50k_neb_S28_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/tal1_1_2500_50k_neb_S28_R2_001.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 - 2018-09-28-plateCUTnRUNtest-TAL1_1_2500_50k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/tal1_1_500_250k_neb_S8_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/tal1_1_500_250k_neb_S8_R2_001.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 - 2018-09-28-plateCUTnRUNtest-TAL1_1_500_250k_neb.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/tal1_1_500_50k_neb_S23_R1_001.fastq.gz /oak/stanford/groups/wjg/seqruns/180926_NB551514_0035_AHYMVNBGX7/Data/Intensities/BaseCalls/tal1_1_500_50k_neb_S23_R2_001.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 - 2018-09-28-plateCUTnRUNtest-TAL1_1_500_50k_neb.2x25mers.hg19.unique