zcat HeLa-S3-CRISPR_E2F1-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 32 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HeLa-S3-CRISPR_E2F1.1x36mers.hg38-no-haps.unique
zcat HeLa-S3-E2F1-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HeLa-S3-E2F1.1x36mers.hg38-no-haps.unique
zcat HeLa-S3-FOS-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HeLa-S3-FOS.1x36mers.hg38-no-haps.unique
zcat HeLa-S3-JUN-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HeLa-S3-JUN.1x36mers.hg38-no-haps.unique
zcat HeLa-S3-JUND-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HeLa-S3-JUND.1x36mers.hg38-no-haps.unique
zcat HepG2-forskolin_pyruvate-1_mM-6.0_hour_6_hour-CEBPB-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-forskolin_pyruvate-1_mM-6.0_hour_6_hour-CEBPB.1x36mers.hg38-no-haps.unique
zcat HepG2-forskolin_pyruvate-1_mM-6.0_hour_6_hour-ESRRA-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-forskolin_pyruvate-1_mM-6.0_hour_6_hour-ESRRA.1x36mers.hg38-no-haps.unique
zcat HepG2-forskolin_pyruvate-1_mM-6.0_hour_6_hour-HSF1-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-forskolin_pyruvate-1_mM-6.0_hour_6_hour-HSF1.1x36mers.hg38-no-haps.unique
zcat HepG2-insulin_22-hydroxycholesterol-10_uM_100_uM-6.0_hour_6_hour-SREBF1-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-insulin_22-hydroxycholesterol-10_uM_100_uM-6.0_hour_6_hour-SREBF1.1x36mers.hg38-no-haps.unique
zcat HepG2-pravastatin-2.0_uM-16.0_hour-SREBF1-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-pravastatin-2.0_uM-16.0_hour-SREBF1.1x36mers.hg38-no-haps.unique
zcat HepG2-ZNF274-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-ZNF274.1x36mers.hg38-no-haps.unique
zcat K562-interferon_alpha6.0_hour-JUN-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-interferon_alpha6.0_hour-JUN.1x36mers.hg38-no-haps.unique
zcat K562-Interferon_gamma30.0_minute-JUN-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-Interferon_gamma30.0_minute-JUN.1x36mers.hg38-no-haps.unique
zcat K562-Interferon_gamma6.0_hour-JUN-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-Interferon_gamma6.0_hour-JUN.1x36mers.hg38-no-haps.unique
zcat K562-ZNF263-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZNF263.1x36mers.hg38-no-haps.unique
zcat MCF-7-CRISPR_E2F1-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 32 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MCF-7-CRISPR_E2F1.1x36mers.hg38-no-haps.unique
zcat endothelial_cell_of_umbilical_vein-JUN-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - endothelial_cell_of_umbilical_vein-JUN.1x36mers.hg38-no-haps.unique
zcat endothelial_cell_of_umbilical_vein-MAX-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - endothelial_cell_of_umbilical_vein-MAX.1x36mers.hg38-no-haps.unique
zcat GM12878-FOS-*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GM12878-FOS.1x36mers.hg38-no-haps.unique