python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_128s_20160517_SH_ScDm_Abf1128s0426-GSM2236872/SRR3925783_1.fastq.gz Cut-and-Run_Abf1_128s_20160517_SH_ScDm_Abf1128s0426-GSM2236872/SRR3925783_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_128s_20160517_SH_ScDm_Abf1128s0426-GSM2236872/SRR3925783.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_128s_2_20160718_SH_ScDm_Abf1_128s630-GSM2265999/SRR4015383_1.fastq.gz Cut-and-Run_Abf1_128s_2_20160718_SH_ScDm_Abf1_128s630-GSM2265999/SRR4015383_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_128s_2_20160718_SH_ScDm_Abf1_128s630-GSM2265999/SRR4015383.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_16s_20160517_SH_ScDm_Abf1_16s0426-GSM2236871/SRR3925782_1.fastq.gz Cut-and-Run_Abf1_16s_20160517_SH_ScDm_Abf1_16s0426-GSM2236871/SRR3925782_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_16s_20160517_SH_ScDm_Abf1_16s0426-GSM2236871/SRR3925782.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_16s_2_20160718_SH_ScDm_Abf1_16s0630-GSM2265995/SRR4015379_1.fastq.gz Cut-and-Run_Abf1_16s_2_20160718_SH_ScDm_Abf1_16s0630-GSM2265995/SRR4015379_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_16s_2_20160718_SH_ScDm_Abf1_16s0630-GSM2265995/SRR4015379.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_1s_20160628_SH_ScDm_Abf1_1s_0426-GSM2236866/SRR3925777_1.fastq.gz Cut-and-Run_Abf1_1s_20160628_SH_ScDm_Abf1_1s_0426-GSM2236866/SRR3925777_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_1s_20160628_SH_ScDm_Abf1_1s_0426-GSM2236866/SRR3925777.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_1s_2_20160718_SH_ScDm_Abf1_1s0630-GSM2265991/SRR4015375_1.fastq.gz Cut-and-Run_Abf1_1s_2_20160718_SH_ScDm_Abf1_1s0630-GSM2265991/SRR4015375_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_1s_2_20160718_SH_ScDm_Abf1_1s0630-GSM2265991/SRR4015375.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_20s_20160909_SH_ScDm_Ab_20s0829-GSM2413644/SRR5071539_1.fastq.gz Cut-and-Run_Abf1_20s_20160909_SH_ScDm_Ab_20s0829-GSM2413644/SRR5071539_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_20s_20160909_SH_ScDm_Ab_20s0829-GSM2413644/SRR5071539.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_20s_Total_20160909_SH_ScDm_Ab_20A0829-GSM2413643/SRR5071538_1.fastq.gz Cut-and-Run_Abf1_20s_Total_20160909_SH_ScDm_Ab_20A0829-GSM2413643/SRR5071538_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_20s_Total_20160909_SH_ScDm_Ab_20A0829-GSM2413643/SRR5071538.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_2s_20160517_SH_ScDm_Abf1_2s_0426-GSM2236867/SRR3925778_1.fastq.gz Cut-and-Run_Abf1_2s_20160517_SH_ScDm_Abf1_2s_0426-GSM2236867/SRR3925778_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_2s_20160517_SH_ScDm_Abf1_2s_0426-GSM2236867/SRR3925778.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_2s_2_20160718_SH_ScDm_Abf1_2s0630-GSM2265992/SRR4015376_1.fastq.gz Cut-and-Run_Abf1_2s_2_20160718_SH_ScDm_Abf1_2s0630-GSM2265992/SRR4015376_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_2s_2_20160718_SH_ScDm_Abf1_2s0630-GSM2265992/SRR4015376.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_32s_20160517_SH_ScDm_Abf1_32s0426-GSM2236870/SRR3925781_1.fastq.gz Cut-and-Run_Abf1_32s_20160517_SH_ScDm_Abf1_32s0426-GSM2236870/SRR3925781_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_32s_20160517_SH_ScDm_Abf1_32s0426-GSM2236870/SRR3925781.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_32s_2_20160718_SH_ScDm_Abf1_32s0630-GSM2265996/SRR4015380_1.fastq.gz Cut-and-Run_Abf1_32s_2_20160718_SH_ScDm_Abf1_32s0630-GSM2265996/SRR4015380_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_32s_2_20160718_SH_ScDm_Abf1_32s0630-GSM2265996/SRR4015380.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_4s_20160517_SH_ScDm_Abf1_4s_0426-GSM2236868/SRR3925779_1.fastq.gz Cut-and-Run_Abf1_4s_20160517_SH_ScDm_Abf1_4s_0426-GSM2236868/SRR3925779_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_4s_20160517_SH_ScDm_Abf1_4s_0426-GSM2236868/SRR3925779.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_4s_2_20160718_SH_ScDm_Abf1_4s0630-GSM2265993/SRR4015377_1.fastq.gz Cut-and-Run_Abf1_4s_2_20160718_SH_ScDm_Abf1_4s0630-GSM2265993/SRR4015377_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_4s_2_20160718_SH_ScDm_Abf1_4s0630-GSM2265993/SRR4015377.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_4s_3_20160909_SH_ScDm_Ab_4s0829-GSM2413645/SRR5071540_1.fastq.gz Cut-and-Run_Abf1_4s_3_20160909_SH_ScDm_Ab_4s0829-GSM2413645/SRR5071540_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_4s_3_20160909_SH_ScDm_Ab_4s0829-GSM2413645/SRR5071540.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_4s_Total_20160909_SH_ScDm_Ab_4A0829-GSM2413646/SRR5071541_1.fastq.gz Cut-and-Run_Abf1_4s_Total_20160909_SH_ScDm_Ab_4A0829-GSM2413646/SRR5071541_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_4s_Total_20160909_SH_ScDm_Ab_4A0829-GSM2413646/SRR5071541.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_64s_20160628_SH_ScDm_Abf1_64s_0426-GSM2265997/SRR4015381_1.fastq.gz Cut-and-Run_Abf1_64s_20160628_SH_ScDm_Abf1_64s_0426-GSM2265997/SRR4015381_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_64s_20160628_SH_ScDm_Abf1_64s_0426-GSM2265997/SRR4015381.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_64s_2_20160718_SH_ScDm_Abf1_64s0630-GSM2265998/SRR4015382_1.fastq.gz Cut-and-Run_Abf1_64s_2_20160718_SH_ScDm_Abf1_64s0630-GSM2265998/SRR4015382_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_64s_2_20160718_SH_ScDm_Abf1_64s0630-GSM2265998/SRR4015382.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_8s_20160517_SH_ScDm_Abf1_8s0426-GSM2236869/SRR3925780_1.fastq.gz Cut-and-Run_Abf1_8s_20160517_SH_ScDm_Abf1_8s0426-GSM2236869/SRR3925780_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_8s_20160517_SH_ScDm_Abf1_8s0426-GSM2236869/SRR3925780.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Abf1_8s_2_20160718_SH_ScDm_Abf1_8s0630-GSM2265994/SRR4015378_1.fastq.gz Cut-and-Run_Abf1_8s_2_20160718_SH_ScDm_Abf1_8s0630-GSM2265994/SRR4015378_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Abf1_8s_2_20160718_SH_ScDm_Abf1_8s0630-GSM2265994/SRR4015378.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse_1m_20160706_SH_ScDm_Cse1m61416-GSM2236883/SRR3925794_1.fastq.gz Cut-and-Run_Cse_1m_20160706_SH_ScDm_Cse1m61416-GSM2236883/SRR3925794_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse_1m_20160706_SH_ScDm_Cse1m61416-GSM2236883/SRR3925794.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse_1mN_20160706_SH_ScDm_Cse1mN61416-GSM2236882/SRR3925793_1.fastq.gz Cut-and-Run_Cse_1mN_20160706_SH_ScDm_Cse1mN61416-GSM2236882/SRR3925793_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse_1mN_20160706_SH_ScDm_Cse1mN61416-GSM2236882/SRR3925793.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse_20s_20160706_SH_ScDm_Cse20s61416-GSM2236881/SRR3925792_1.fastq.gz Cut-and-Run_Cse_20s_20160706_SH_ScDm_Cse20s61416-GSM2236881/SRR3925792_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse_20s_20160706_SH_ScDm_Cse20s61416-GSM2236881/SRR3925792.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse_20sN_20160706_SH_ScDm_Cse20sN61416-GSM2236880/SRR3925791_1.fastq.gz Cut-and-Run_Cse_20sN_20160706_SH_ScDm_Cse20sN61416-GSM2236880/SRR3925791_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse_20sN_20160706_SH_ScDm_Cse20sN61416-GSM2236880/SRR3925791.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse_3m_20160706_SH_ScDm_Cse3m61416-GSM2236885/SRR3925796_1.fastq.gz Cut-and-Run_Cse_3m_20160706_SH_ScDm_Cse3m61416-GSM2236885/SRR3925796_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse_3m_20160706_SH_ScDm_Cse3m61416-GSM2236885/SRR3925796.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse_3mN_20160706_SH_ScDm_Cse3mN61416-GSM2236884/SRR3925795_1.fastq.gz Cut-and-Run_Cse_3mN_20160706_SH_ScDm_Cse3mN61416-GSM2236884/SRR3925795_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse_3mN_20160706_SH_ScDm_Cse3mN61416-GSM2236884/SRR3925795.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse4_100s_20160909_SH_ScDm_Cs_100s0829-GSM2413648/SRR5071543_1.fastq.gz Cut-and-Run_Cse4_100s_20160909_SH_ScDm_Cs_100s0829-GSM2413648/SRR5071543_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse4_100s_20160909_SH_ScDm_Cs_100s0829-GSM2413648/SRR5071543.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse4_100s_Total_20160909_SH_ScDm_Cs_100A0829-GSM2413647/SRR5071542_1.fastq.gz Cut-and-Run_Cse4_100s_Total_20160909_SH_ScDm_Cs_100A0829-GSM2413647/SRR5071542_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse4_100s_Total_20160909_SH_ScDm_Cs_100A0829-GSM2413647/SRR5071542.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse4_20s_20160909_SH_ScDm_Cs_20s0829-GSM2413650/SRR5071545_1.fastq.gz Cut-and-Run_Cse4_20s_20160909_SH_ScDm_Cs_20s0829-GSM2413650/SRR5071545_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse4_20s_20160909_SH_ScDm_Cs_20s0829-GSM2413650/SRR5071545.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse4_20s_Total_20160909_SH_ScDm_Cs_20A0829-GSM2413649/SRR5071544_1.fastq.gz Cut-and-Run_Cse4_20s_Total_20160909_SH_ScDm_Cs_20A0829-GSM2413649/SRR5071544_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse4_20s_Total_20160909_SH_ScDm_Cs_20A0829-GSM2413649/SRR5071544.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse4_2500s_20160909_SH_ScDm_Cs_2500s0829-GSM2413652/SRR5071547_1.fastq.gz Cut-and-Run_Cse4_2500s_20160909_SH_ScDm_Cs_2500s0829-GSM2413652/SRR5071547_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse4_2500s_20160909_SH_ScDm_Cs_2500s0829-GSM2413652/SRR5071547.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse4_2500s_Total_20160909_SH_ScDm_Cs_2500A0829-GSM2413651/SRR5071546_1.fastq.gz Cut-and-Run_Cse4_2500s_Total_20160909_SH_ScDm_Cs_2500A0829-GSM2413651/SRR5071546_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse4_2500s_Total_20160909_SH_ScDm_Cs_2500A0829-GSM2413651/SRR5071546.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse4_500s_20160909_SH_ScDm_Cs_500s0829-GSM2413654/SRR5071549_1.fastq.gz Cut-and-Run_Cse4_500s_20160909_SH_ScDm_Cs_500s0829-GSM2413654/SRR5071549_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse4_500s_20160909_SH_ScDm_Cs_500s0829-GSM2413654/SRR5071549.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse4_500s_Total_20160909_SH_ScDm_Cs_500A0829-GSM2413653/SRR5071548_1.fastq.gz Cut-and-Run_Cse4_500s_Total_20160909_SH_ScDm_Cs_500A0829-GSM2413653/SRR5071548_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse4_500s_Total_20160909_SH_ScDm_Cs_500A0829-GSM2413653/SRR5071548.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse4_X-link_10m_Total_20160916_SH_ScDm_Cse4px10m825-GSM2413655/SRR5071550_1.fastq.gz Cut-and-Run_Cse4_X-link_10m_Total_20160916_SH_ScDm_Cse4px10m825-GSM2413655/SRR5071550_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse4_X-link_10m_Total_20160916_SH_ScDm_Cse4px10m825-GSM2413655/SRR5071550.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse4_X-link_1m_Total_20160916_SH_ScDm_Cse4px1m825-GSM2413656/SRR5071551_1.fastq.gz Cut-and-Run_Cse4_X-link_1m_Total_20160916_SH_ScDm_Cse4px1m825-GSM2413656/SRR5071551_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse4_X-link_1m_Total_20160916_SH_ScDm_Cse4px1m825-GSM2413656/SRR5071551.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse4_X-link_20s_Total_20160916_SH_ScDm_Cse4px20s825-GSM2413657/SRR5071552_1.fastq.gz Cut-and-Run_Cse4_X-link_20s_Total_20160916_SH_ScDm_Cse4px20s825-GSM2413657/SRR5071552_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse4_X-link_20s_Total_20160916_SH_ScDm_Cse4px20s825-GSM2413657/SRR5071552.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Cse4_X-link_3m_Total_20160916_SH_ScDm_Cse4px3m825-GSM2413658/SRR5071553_1.fastq.gz Cut-and-Run_Cse4_X-link_3m_Total_20160916_SH_ScDm_Cse4px3m825-GSM2413658/SRR5071553_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Cse4_X-link_3m_Total_20160916_SH_ScDm_Cse4px3m825-GSM2413658/SRR5071553.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_100s_20160909_SH_ScDm_H2_100s0829-GSM2413660/SRR5071556_1.fastq.gz Cut-and-Run_H2A_100s_20160909_SH_ScDm_H2_100s0829-GSM2413660/SRR5071556_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_100s_20160909_SH_ScDm_H2_100s0829-GSM2413660/SRR5071556.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_100s_Total_20160909_SH_ScDm_H2_100A0829-GSM2413659/SRR5071555_1.fastq.gz Cut-and-Run_H2A_100s_Total_20160909_SH_ScDm_H2_100A0829-GSM2413659/SRR5071555_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_100s_Total_20160909_SH_ScDm_H2_100A0829-GSM2413659/SRR5071555.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_1m_20160706_SH_ScDm_H2A1m61416-GSM2236889/SRR3925800_1.fastq.gz Cut-and-Run_H2A_1m_20160706_SH_ScDm_H2A1m61416-GSM2236889/SRR3925800_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_1m_20160706_SH_ScDm_H2A1m61416-GSM2236889/SRR3925800.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_1mN_20160706_SH_ScDm_H2A1mN61416-GSM2236888/SRR3925799_1.fastq.gz Cut-and-Run_H2A_1mN_20160706_SH_ScDm_H2A1mN61416-GSM2236888/SRR3925799_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_1mN_20160706_SH_ScDm_H2A1mN61416-GSM2236888/SRR3925799.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_20s_20160706_SH_ScDm_H2A20s61416-GSM2236887/SRR3925798_1.fastq.gz Cut-and-Run_H2A_20s_20160706_SH_ScDm_H2A20s61416-GSM2236887/SRR3925798_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_20s_20160706_SH_ScDm_H2A20s61416-GSM2236887/SRR3925798.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_20s_2_20160909_SH_ScDm_H2_20s0829-GSM2413661/SRR5071557_1.fastq.gz Cut-and-Run_H2A_20s_2_20160909_SH_ScDm_H2_20s0829-GSM2413661/SRR5071557_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_20s_2_20160909_SH_ScDm_H2_20s0829-GSM2413661/SRR5071557.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_20sN_20160706_SH_ScDm_H2A20sN61416-GSM2236886/SRR3925797_1.fastq.gz Cut-and-Run_H2A_20sN_20160706_SH_ScDm_H2A20sN61416-GSM2236886/SRR3925797_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_20sN_20160706_SH_ScDm_H2A20sN61416-GSM2236886/SRR3925797.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_20s_Total_20160909_SH_ScDm_H2_20A0829-GSM2413662/SRR5071558_1.fastq.gz Cut-and-Run_H2A_20s_Total_20160909_SH_ScDm_H2_20A0829-GSM2413662/SRR5071558_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_20s_Total_20160909_SH_ScDm_H2_20A0829-GSM2413662/SRR5071558.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_2500s_20160909_SH_ScDm_H2_2500s0829-GSM2413664/SRR5071560_1.fastq.gz Cut-and-Run_H2A_2500s_20160909_SH_ScDm_H2_2500s0829-GSM2413664/SRR5071560_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_2500s_20160909_SH_ScDm_H2_2500s0829-GSM2413664/SRR5071560.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_2500s_Total_20160909_SH_ScDm_H2_2500A0829-GSM2413663/SRR5071559_1.fastq.gz Cut-and-Run_H2A_2500s_Total_20160909_SH_ScDm_H2_2500A0829-GSM2413663/SRR5071559_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_2500s_Total_20160909_SH_ScDm_H2_2500A0829-GSM2413663/SRR5071559.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_3m_20160706_SH_ScDm_H2A3m61416-GSM2236891/SRR3925802_1.fastq.gz Cut-and-Run_H2A_3m_20160706_SH_ScDm_H2A3m61416-GSM2236891/SRR3925802_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_3m_20160706_SH_ScDm_H2A3m61416-GSM2236891/SRR3925802.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_3mN_20160706_SH_ScDm_H2A3mN61416-GSM2236890/SRR3925801_1.fastq.gz Cut-and-Run_H2A_3mN_20160706_SH_ScDm_H2A3mN61416-GSM2236890/SRR3925801_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_3mN_20160706_SH_ScDm_H2A3mN61416-GSM2236890/SRR3925801.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_500s_20160909_SH_ScDm_H2_500s0829-GSM2413666/SRR5071562_1.fastq.gz Cut-and-Run_H2A_500s_20160909_SH_ScDm_H2_500s0829-GSM2413666/SRR5071562_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_500s_20160909_SH_ScDm_H2_500s0829-GSM2413666/SRR5071562.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_500s_Total_20160909_SH_ScDm_H2_500A0829-GSM2413665/SRR5071561_1.fastq.gz Cut-and-Run_H2A_500s_Total_20160909_SH_ScDm_H2_500A0829-GSM2413665/SRR5071561_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_500s_Total_20160909_SH_ScDm_H2_500A0829-GSM2413665/SRR5071561.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_X-link_10m_Total_20160916_SH_ScDm_H2Apx10m825-GSM2413667/SRR5071563_1.fastq.gz Cut-and-Run_H2A_X-link_10m_Total_20160916_SH_ScDm_H2Apx10m825-GSM2413667/SRR5071563_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_X-link_10m_Total_20160916_SH_ScDm_H2Apx10m825-GSM2413667/SRR5071563.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_X-link_1m_Total_20160916_SH_ScDm_H2Apx1m825-GSM2413668/SRR5071564_1.fastq.gz Cut-and-Run_H2A_X-link_1m_Total_20160916_SH_ScDm_H2Apx1m825-GSM2413668/SRR5071564_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_X-link_1m_Total_20160916_SH_ScDm_H2Apx1m825-GSM2413668/SRR5071564.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_X-link_20s_Total_20160916_SH_ScDm_H2Apx20s825-GSM2413669/SRR5071565_1.fastq.gz Cut-and-Run_H2A_X-link_20s_Total_20160916_SH_ScDm_H2Apx20s825-GSM2413669/SRR5071565_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_X-link_20s_Total_20160916_SH_ScDm_H2Apx20s825-GSM2413669/SRR5071565.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_H2A_X-link_3m_Total_20160916_SH_ScDm_H2Apx3m825-GSM2413670/SRR5071566_1.fastq.gz Cut-and-Run_H2A_X-link_3m_Total_20160916_SH_ScDm_H2Apx3m825-GSM2413670/SRR5071566_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_H2A_X-link_3m_Total_20160916_SH_ScDm_H2Apx3m825-GSM2413670/SRR5071566.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Mot1_10m_Total_20161123_SH_ScDm_Mot110m_1107-GSM2413671/SRR5071567_1.fastq.gz Cut-and-Run_Mot1_10m_Total_20161123_SH_ScDm_Mot110m_1107-GSM2413671/SRR5071567_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Mot1_10m_Total_20161123_SH_ScDm_Mot110m_1107-GSM2413671/SRR5071567.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Mot1_1m_Total_20161123_SH_ScDm_Mot11m_1107-GSM2413672/SRR5071568_1.fastq.gz Cut-and-Run_Mot1_1m_Total_20161123_SH_ScDm_Mot11m_1107-GSM2413672/SRR5071568_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Mot1_1m_Total_20161123_SH_ScDm_Mot11m_1107-GSM2413672/SRR5071568.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Mot1_20s_Total_20161123_SH_ScDm_Mot120s_1107-GSM2413673/SRR5071569_1.fastq.gz Cut-and-Run_Mot1_20s_Total_20161123_SH_ScDm_Mot120s_1107-GSM2413673/SRR5071569_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Mot1_20s_Total_20161123_SH_ScDm_Mot120s_1107-GSM2413673/SRR5071569.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Mot1_3m_Total_20161123_SH_ScDm_Mot13m_1107-GSM2413674/SRR5071570_1.fastq.gz Cut-and-Run_Mot1_3m_Total_20161123_SH_ScDm_Mot13m_1107-GSM2413674/SRR5071570_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Mot1_3m_Total_20161123_SH_ScDm_Mot13m_1107-GSM2413674/SRR5071570.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Mot1_5s_Total_20161123_SH_ScDm_Mot15s_1107-GSM2413675/SRR5071571_1.fastq.gz Cut-and-Run_Mot1_5s_Total_20161123_SH_ScDm_Mot15s_1107-GSM2413675/SRR5071571_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Mot1_5s_Total_20161123_SH_ScDm_Mot15s_1107-GSM2413675/SRR5071571.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Mot1_No1o_Total_20161123_SH_ScDm_Mot1No1_1107-GSM2413676/SRR5071572_1.fastq.gz Cut-and-Run_Mot1_No1o_Total_20161123_SH_ScDm_Mot1No1_1107-GSM2413676/SRR5071572_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Mot1_No1o_Total_20161123_SH_ScDm_Mot1No1_1107-GSM2413676/SRR5071572.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_128s_20160517_SH_ScDm_Reb1128s0426-GSM2236879/SRR3925790_1.fastq.gz Cut-and-Run_Reb1_128s_20160517_SH_ScDm_Reb1128s0426-GSM2236879/SRR3925790_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_128s_20160517_SH_ScDm_Reb1128s0426-GSM2236879/SRR3925790.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_128s_2_20160718_SH_ScDm_Reb1_128s630-GSM2266008/SRR4015392_1.fastq.gz Cut-and-Run_Reb1_128s_2_20160718_SH_ScDm_Reb1_128s630-GSM2266008/SRR4015392_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_128s_2_20160718_SH_ScDm_Reb1_128s630-GSM2266008/SRR4015392.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_16s_20160517_SH_ScDm_Reb1_16s0426-GSM2236878/SRR3925789_1.fastq.gz Cut-and-Run_Reb1_16s_20160517_SH_ScDm_Reb1_16s0426-GSM2236878/SRR3925789_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_16s_20160517_SH_ScDm_Reb1_16s0426-GSM2236878/SRR3925789.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_16s_2_20160718_SH_ScDm_Reb1_16s0630-GSM2266004/SRR4015388_1.fastq.gz Cut-and-Run_Reb1_16s_2_20160718_SH_ScDm_Reb1_16s0630-GSM2266004/SRR4015388_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_16s_2_20160718_SH_ScDm_Reb1_16s0630-GSM2266004/SRR4015388.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_1s_20160628_SH_ScDm_Reb1_1s_0426-GSM2236873/SRR3925784_1.fastq.gz Cut-and-Run_Reb1_1s_20160628_SH_ScDm_Reb1_1s_0426-GSM2236873/SRR3925784_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_1s_20160628_SH_ScDm_Reb1_1s_0426-GSM2236873/SRR3925784.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_1s_2_20160718_SH_ScDm_Reb1_1s0630-GSM2266000/SRR4015384_1.fastq.gz Cut-and-Run_Reb1_1s_2_20160718_SH_ScDm_Reb1_1s0630-GSM2266000/SRR4015384_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_1s_2_20160718_SH_ScDm_Reb1_1s0630-GSM2266000/SRR4015384.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_20s_20160909_SH_ScDm_Re_20s0829-GSM2413678/SRR5071574_1.fastq.gz Cut-and-Run_Reb1_20s_20160909_SH_ScDm_Re_20s0829-GSM2413678/SRR5071574_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_20s_20160909_SH_ScDm_Re_20s0829-GSM2413678/SRR5071574.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_20s_Total_20160909_SH_ScDm_Re_20A0829-GSM2413677/SRR5071573_1.fastq.gz Cut-and-Run_Reb1_20s_Total_20160909_SH_ScDm_Re_20A0829-GSM2413677/SRR5071573_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_20s_Total_20160909_SH_ScDm_Re_20A0829-GSM2413677/SRR5071573.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_2s_20160517_SH_ScDm_Reb1_2s_0426-GSM2236874/SRR3925785_1.fastq.gz Cut-and-Run_Reb1_2s_20160517_SH_ScDm_Reb1_2s_0426-GSM2236874/SRR3925785_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_2s_20160517_SH_ScDm_Reb1_2s_0426-GSM2236874/SRR3925785.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_2s_2_20160718_SH_ScDm_Reb1_2s0630-GSM2266001/SRR4015385_1.fastq.gz Cut-and-Run_Reb1_2s_2_20160718_SH_ScDm_Reb1_2s0630-GSM2266001/SRR4015385_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_2s_2_20160718_SH_ScDm_Reb1_2s0630-GSM2266001/SRR4015385.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_32s_20160517_SH_ScDm_Reb1_32s0426-GSM2236877/SRR3925788_1.fastq.gz Cut-and-Run_Reb1_32s_20160517_SH_ScDm_Reb1_32s0426-GSM2236877/SRR3925788_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_32s_20160517_SH_ScDm_Reb1_32s0426-GSM2236877/SRR3925788.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_32s_2_20160718_SH_ScDm_Reb1_32s0630-GSM2266005/SRR4015389_1.fastq.gz Cut-and-Run_Reb1_32s_2_20160718_SH_ScDm_Reb1_32s0630-GSM2266005/SRR4015389_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_32s_2_20160718_SH_ScDm_Reb1_32s0630-GSM2266005/SRR4015389.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_4s_20160517_SH_ScDm_Reb1_4s_0426-GSM2236875/SRR3925786_1.fastq.gz Cut-and-Run_Reb1_4s_20160517_SH_ScDm_Reb1_4s_0426-GSM2236875/SRR3925786_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_4s_20160517_SH_ScDm_Reb1_4s_0426-GSM2236875/SRR3925786.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_4s_2_20160718_SH_ScDm_Reb1_4s0630-GSM2266002/SRR4015386_1.fastq.gz Cut-and-Run_Reb1_4s_2_20160718_SH_ScDm_Reb1_4s0630-GSM2266002/SRR4015386_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_4s_2_20160718_SH_ScDm_Reb1_4s0630-GSM2266002/SRR4015386.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_4s_3_20160909_SH_ScDm_Re_4s0829-GSM2413679/SRR5071575_1.fastq.gz Cut-and-Run_Reb1_4s_3_20160909_SH_ScDm_Re_4s0829-GSM2413679/SRR5071575_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_4s_3_20160909_SH_ScDm_Re_4s0829-GSM2413679/SRR5071575.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_4s_Total_20160909_SH_ScDm_Re_4A0829-GSM2413680/SRR5071554_1.fastq.gz Cut-and-Run_Reb1_4s_Total_20160909_SH_ScDm_Re_4A0829-GSM2413680/SRR5071554_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_4s_Total_20160909_SH_ScDm_Re_4A0829-GSM2413680/SRR5071554.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_64s_20160718_SH_ScDm_Reb1_64s_0426-GSM2266006/SRR4015390_1.fastq.gz Cut-and-Run_Reb1_64s_20160718_SH_ScDm_Reb1_64s_0426-GSM2266006/SRR4015390_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_64s_20160718_SH_ScDm_Reb1_64s_0426-GSM2266006/SRR4015390.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_64s_2_20160718_SH_ScDm_Reb1_64s0630-GSM2266007/SRR4015391_1.fastq.gz Cut-and-Run_Reb1_64s_2_20160718_SH_ScDm_Reb1_64s0630-GSM2266007/SRR4015391_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_64s_2_20160718_SH_ScDm_Reb1_64s0630-GSM2266007/SRR4015391.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_8s_20160517_SH_ScDm_Reb1_8s0426-GSM2236876/SRR3925787_1.fastq.gz Cut-and-Run_Reb1_8s_20160517_SH_ScDm_Reb1_8s0426-GSM2236876/SRR3925787_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_8s_20160517_SH_ScDm_Reb1_8s0426-GSM2236876/SRR3925787.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Reb1_8s_2_20160718_SH_ScDm_Reb1_8s0630-GSM2266003/SRR4015387_1.fastq.gz Cut-and-Run_Reb1_8s_2_20160718_SH_ScDm_Reb1_8s0630-GSM2266003/SRR4015387_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Reb1_8s_2_20160718_SH_ScDm_Reb1_8s0630-GSM2266003/SRR4015387.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Sth1_10m_Total_1_20161123_SH_ScDm_Sth110m_1104-GSM2413681/SRR5071576_1.fastq.gz Cut-and-Run_Sth1_10m_Total_1_20161123_SH_ScDm_Sth110m_1104-GSM2413681/SRR5071576_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Sth1_10m_Total_1_20161123_SH_ScDm_Sth110m_1104-GSM2413681/SRR5071576.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Sth1_10m_Total_2_20161123_SH_ScDm_Sth110m_1107-GSM2413682/SRR5071577_1.fastq.gz Cut-and-Run_Sth1_10m_Total_2_20161123_SH_ScDm_Sth110m_1107-GSM2413682/SRR5071577_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Sth1_10m_Total_2_20161123_SH_ScDm_Sth110m_1107-GSM2413682/SRR5071577.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Sth1_1m_Total_1_20161123_SH_ScDm_Sth11m_1104-GSM2413683/SRR5071578_1.fastq.gz Cut-and-Run_Sth1_1m_Total_1_20161123_SH_ScDm_Sth11m_1104-GSM2413683/SRR5071578_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Sth1_1m_Total_1_20161123_SH_ScDm_Sth11m_1104-GSM2413683/SRR5071578.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Sth1_1m_Total_2_20161123_SH_ScDm_Sth11m_1107-GSM2413684/SRR5071579_1.fastq.gz Cut-and-Run_Sth1_1m_Total_2_20161123_SH_ScDm_Sth11m_1107-GSM2413684/SRR5071579_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Sth1_1m_Total_2_20161123_SH_ScDm_Sth11m_1107-GSM2413684/SRR5071579.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Sth1_20s_Total_1_20161123_SH_ScDm_Sth120s_1104-GSM2413685/SRR5071580_1.fastq.gz Cut-and-Run_Sth1_20s_Total_1_20161123_SH_ScDm_Sth120s_1104-GSM2413685/SRR5071580_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Sth1_20s_Total_1_20161123_SH_ScDm_Sth120s_1104-GSM2413685/SRR5071580.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Sth1_20s_Total_2_20161123_SH_ScDm_Sth120s_1107-GSM2413686/SRR5071581_1.fastq.gz Cut-and-Run_Sth1_20s_Total_2_20161123_SH_ScDm_Sth120s_1107-GSM2413686/SRR5071581_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Sth1_20s_Total_2_20161123_SH_ScDm_Sth120s_1107-GSM2413686/SRR5071581.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Sth1_30m_Total_20161123_SH_ScDm_Sth130m_1107-GSM2413687/SRR5071582_1.fastq.gz Cut-and-Run_Sth1_30m_Total_20161123_SH_ScDm_Sth130m_1107-GSM2413687/SRR5071582_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Sth1_30m_Total_20161123_SH_ScDm_Sth130m_1107-GSM2413687/SRR5071582.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Sth1_3m_Total_1_20161123_SH_ScDm_Sth13m_1104-GSM2413688/SRR5071583_1.fastq.gz Cut-and-Run_Sth1_3m_Total_1_20161123_SH_ScDm_Sth13m_1104-GSM2413688/SRR5071583_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Sth1_3m_Total_1_20161123_SH_ScDm_Sth13m_1104-GSM2413688/SRR5071583.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Sth1_3m_Total_2_20161123_SH_ScDm_Sth13m_1107-GSM2413689/SRR5071584_1.fastq.gz Cut-and-Run_Sth1_3m_Total_2_20161123_SH_ScDm_Sth13m_1107-GSM2413689/SRR5071584_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Sth1_3m_Total_2_20161123_SH_ScDm_Sth13m_1107-GSM2413689/SRR5071584.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Sth1_5s_Total_20161123_SH_ScDm_Sth15s_1104-GSM2413690/SRR5071585_1.fastq.gz Cut-and-Run_Sth1_5s_Total_20161123_SH_ScDm_Sth15s_1104-GSM2413690/SRR5071585_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Sth1_5s_Total_20161123_SH_ScDm_Sth15s_1104-GSM2413690/SRR5071585.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Sth1_No1o_Total_1_20161123_SH_ScDm_Sth1No1_1104-GSM2413691/SRR5071586_1.fastq.gz Cut-and-Run_Sth1_No1o_Total_1_20161123_SH_ScDm_Sth1No1_1104-GSM2413691/SRR5071586_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Sth1_No1o_Total_1_20161123_SH_ScDm_Sth1No1_1104-GSM2413691/SRR5071586.2x25mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Cut-and-Run_Sth1_No1o_Total_2_20161123_SH_ScDm_Sth1no1_1107-GSM2413692/SRR5071587_1.fastq.gz Cut-and-Run_Sth1_No1o_Total_2_20161123_SH_ScDm_Sth1no1_1107-GSM2413692/SRR5071587_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -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/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cut-and-Run_Sth1_No1o_Total_2_20161123_SH_ScDm_Sth1no1_1107-GSM2413692/SRR5071587.2x25mers.unique