python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_H3K27ac_plasmid_1-GSM2648945/SRR5642859_1.fastq.gz naive_H3K27ac_plasmid_1-GSM2648945/SRR5642859_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_H3K27ac_plasmid_1-GSM2648945/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_H3K4me1_plasmid_1-GSM2648947/SRR5642861_1.fastq.gz naive_H3K4me1_plasmid_1-GSM2648947/SRR5642861_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_H3K4me1_plasmid_1-GSM2648947/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_naive_H3K27ac_RNA_1-GSM2648954/SRR5642868_1.fastq.gz naive_naive_H3K27ac_RNA_1-GSM2648954/SRR5642868_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_naive_H3K27ac_RNA_1-GSM2648954/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_naive_H3K27ac_RNA_2-GSM2648955/SRR5642869_1.fastq.gz naive_naive_H3K27ac_RNA_2-GSM2648955/SRR5642869_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_naive_H3K27ac_RNA_2-GSM2648955/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_naive_H3K4me1_RNA_1-GSM2648958/SRR5642872_1.fastq.gz naive_naive_H3K4me1_RNA_1-GSM2648958/SRR5642872_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_naive_H3K4me1_RNA_1-GSM2648958/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_naive_H3K4me1_RNA_2-GSM2648959/SRR5642873_1.fastq.gz naive_naive_H3K4me1_RNA_2-GSM2648959/SRR5642873_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_naive_H3K4me1_RNA_2-GSM2648959/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_naive_Nanog_RNA_1-GSM2648966/SRR5642880_1.fastq.gz naive_naive_Nanog_RNA_1-GSM2648966/SRR5642880_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_naive_Nanog_RNA_1-GSM2648966/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_naive_Nanog_RNA_2-GSM2648967/SRR5642881_1.fastq.gz naive_naive_Nanog_RNA_2-GSM2648967/SRR5642881_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_naive_Nanog_RNA_2-GSM2648967/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_naive_Oct4_RNA_1-GSM2648974/SRR5642888_1.fastq.gz naive_naive_Oct4_RNA_1-GSM2648974/SRR5642888_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_naive_Oct4_RNA_1-GSM2648974/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_naive_Oct4_RNA_2-GSM2648975/SRR5642889_1.fastq.gz naive_naive_Oct4_RNA_2-GSM2648975/SRR5642889_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_naive_Oct4_RNA_2-GSM2648975/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_Nanog_plasmid_1-GSM2648950/SRR5642864_1.fastq.gz naive_Nanog_plasmid_1-GSM2648950/SRR5642864_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_Nanog_plasmid_1-GSM2648950/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_Oct4_plasmid_1-GSM2648952/SRR5642866_1.fastq.gz naive_Oct4_plasmid_1-GSM2648952/SRR5642866_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_Oct4_plasmid_1-GSM2648952/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_primed_Nanog_RNA_1-GSM2648968/SRR5642882_1.fastq.gz naive_primed_Nanog_RNA_1-GSM2648968/SRR5642882_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_primed_Nanog_RNA_1-GSM2648968/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_primed_Nanog_RNA_2-GSM2648969/SRR5642883_1.fastq.gz naive_primed_Nanog_RNA_2-GSM2648969/SRR5642883_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_primed_Nanog_RNA_2-GSM2648969/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_primed_Oct4_RNA_1-GSM2648976/SRR5642890_1.fastq.gz naive_primed_Oct4_RNA_1-GSM2648976/SRR5642890_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_primed_Oct4_RNA_1-GSM2648976/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py naive_primed_Oct4_RNA_2-GSM2648977/SRR5642891_1.fastq.gz naive_primed_Oct4_RNA_2-GSM2648977/SRR5642891_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - naive_primed_Oct4_RNA_2-GSM2648977/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_H3K27ac_plasmid_1-GSM2648946/SRR5642860_1.fastq.gz primed_H3K27ac_plasmid_1-GSM2648946/SRR5642860_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_H3K27ac_plasmid_1-GSM2648946/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_H3K4me1_plasmid_1-GSM2648948/SRR5642862_1.fastq.gz primed_H3K4me1_plasmid_1-GSM2648948/SRR5642862_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_H3K4me1_plasmid_1-GSM2648948/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_Input_plasmid_1-GSM2648949/SRR5642863_1.fastq.gz primed_Input_plasmid_1-GSM2648949/SRR5642863_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_Input_plasmid_1-GSM2648949/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_naive_Input_RNA_1-GSM2648962/SRR5642876_1.fastq.gz primed_naive_Input_RNA_1-GSM2648962/SRR5642876_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_naive_Input_RNA_1-GSM2648962/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_naive_Input_RNA_2-GSM2648963/SRR5642877_1.fastq.gz primed_naive_Input_RNA_2-GSM2648963/SRR5642877_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_naive_Input_RNA_2-GSM2648963/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_naive_Nanog_RNA_1-GSM2648970/SRR5642884_1.fastq.gz primed_naive_Nanog_RNA_1-GSM2648970/SRR5642884_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_naive_Nanog_RNA_1-GSM2648970/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_naive_Nanog_RNA_2-GSM2648971/SRR5642885_1.fastq.gz primed_naive_Nanog_RNA_2-GSM2648971/SRR5642885_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_naive_Nanog_RNA_2-GSM2648971/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_naive_Oct4_RNA_1-GSM2648978/SRR5642892_1.fastq.gz primed_naive_Oct4_RNA_1-GSM2648978/SRR5642892_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_naive_Oct4_RNA_1-GSM2648978/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_naive_Oct4_RNA_2-GSM2648979/SRR5642893_1.fastq.gz primed_naive_Oct4_RNA_2-GSM2648979/SRR5642893_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_naive_Oct4_RNA_2-GSM2648979/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_Nanog_plasmid_1-GSM2648951/SRR5642865_1.fastq.gz primed_Nanog_plasmid_1-GSM2648951/SRR5642865_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_Nanog_plasmid_1-GSM2648951/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_Oct4_plasmid_1-GSM2648953/SRR5642867_1.fastq.gz primed_Oct4_plasmid_1-GSM2648953/SRR5642867_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_Oct4_plasmid_1-GSM2648953/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_H3K27ac_extplasmid_1-GSM2648935/SRR5642849_1.fastq.gz primed_primed_H3K27ac_extplasmid_1-GSM2648935/SRR5642849_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_H3K27ac_extplasmid_1-GSM2648935/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_H3K27ac_extplasmid_2-GSM2648936/SRR5642850_1.fastq.gz primed_primed_H3K27ac_extplasmid_2-GSM2648936/SRR5642850_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_H3K27ac_extplasmid_2-GSM2648936/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_H3K27ac_RNA_1-GSM2648956/SRR5642870_1.fastq.gz primed_primed_H3K27ac_RNA_1-GSM2648956/SRR5642870_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_H3K27ac_RNA_1-GSM2648956/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_H3K27ac_RNA_2-GSM2648957/SRR5642871_1.fastq.gz primed_primed_H3K27ac_RNA_2-GSM2648957/SRR5642871_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_H3K27ac_RNA_2-GSM2648957/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_H3K4me1_extplasmid_1-GSM2648937/SRR5642851_1.fastq.gz primed_primed_H3K4me1_extplasmid_1-GSM2648937/SRR5642851_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_H3K4me1_extplasmid_1-GSM2648937/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_H3K4me1_extplasmid_2-GSM2648938/SRR5642852_1.fastq.gz primed_primed_H3K4me1_extplasmid_2-GSM2648938/SRR5642852_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_H3K4me1_extplasmid_2-GSM2648938/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_H3K4me1_RNA_1-GSM2648960/SRR5642874_1.fastq.gz primed_primed_H3K4me1_RNA_1-GSM2648960/SRR5642874_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_H3K4me1_RNA_1-GSM2648960/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_H3K4me1_RNA_2-GSM2648961/SRR5642875_1.fastq.gz primed_primed_H3K4me1_RNA_2-GSM2648961/SRR5642875_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_H3K4me1_RNA_2-GSM2648961/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_Input_extplasmid_1-GSM2648939/SRR5642853_1.fastq.gz primed_primed_Input_extplasmid_1-GSM2648939/SRR5642853_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_Input_extplasmid_1-GSM2648939/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_Input_extplasmid_2-GSM2648940/SRR5642854_1.fastq.gz primed_primed_Input_extplasmid_2-GSM2648940/SRR5642854_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_Input_extplasmid_2-GSM2648940/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_Input_RNA_1-GSM2648964/SRR5642878_1.fastq.gz primed_primed_Input_RNA_1-GSM2648964/SRR5642878_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_Input_RNA_1-GSM2648964/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_Input_RNA_2-GSM2648965/SRR5642879_1.fastq.gz primed_primed_Input_RNA_2-GSM2648965/SRR5642879_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_Input_RNA_2-GSM2648965/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_Nanog_extplasmid_1-GSM2648941/SRR5642855_1.fastq.gz primed_primed_Nanog_extplasmid_1-GSM2648941/SRR5642855_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_Nanog_extplasmid_1-GSM2648941/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_Nanog_extplasmid_2-GSM2648942/SRR5642856_1.fastq.gz primed_primed_Nanog_extplasmid_2-GSM2648942/SRR5642856_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_Nanog_extplasmid_2-GSM2648942/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_Nanog_RNA_1-GSM2648972/SRR5642886_1.fastq.gz primed_primed_Nanog_RNA_1-GSM2648972/SRR5642886_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_Nanog_RNA_1-GSM2648972/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_Nanog_RNA_2-GSM2648973/SRR5642887_1.fastq.gz primed_primed_Nanog_RNA_2-GSM2648973/SRR5642887_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_Nanog_RNA_2-GSM2648973/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_Oct4_extplasmid_1-GSM2648943/SRR5642857_1.fastq.gz primed_primed_Oct4_extplasmid_1-GSM2648943/SRR5642857_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_Oct4_extplasmid_1-GSM2648943/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_Oct4_extplasmid_2-GSM2648944/SRR5642858_1.fastq.gz primed_primed_Oct4_extplasmid_2-GSM2648944/SRR5642858_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_Oct4_extplasmid_2-GSM2648944/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_Oct4_RNA_1-GSM2648980/SRR5642894_1.fastq.gz primed_primed_Oct4_RNA_1-GSM2648980/SRR5642894_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_Oct4_RNA_1-GSM2648980/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py primed_primed_Oct4_RNA_2-GSM2648981/SRR5642895_1.fastq.gz primed_primed_Oct4_RNA_2-GSM2648981/SRR5642895_2.fastq.gz -trim 36 36 | /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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - primed_primed_Oct4_RNA_2-GSM2648981/alignments.2x36mers.unique