python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L3752-Hanbang_Zhan_U-HP_NRSF/L3752-Hanbang_Zhan_U-HP_NRSF.250413_NB551514_0281_AHHLNJBGXW.end1.fastq.gz,L3752-Hanbang_Zhan_U-HP_NRSF.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3752-Hanbang_Zhan_U-HP_NRSF.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L3753-Hanbang_Zhan_U-HP_NRSF/L3753-Hanbang_Zhan_U-HP_NRSF.250413_NB551514_0281_AHHLNJBGXW.end1.fastq.gz,L3753-Hanbang_Zhan_U-HP_NRSF.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3753-Hanbang_Zhan_U-HP_NRSF.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L3754-Hanbang_Zhan_U-O_NRSF/L3754-Hanbang_Zhan_U-O_NRSF.250413_NB551514_0281_AHHLNJBGXW.end1.fastq.gz,L3754-Hanbang_Zhan_U-O_NRSF.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3754-Hanbang_Zhan_U-O_NRSF.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L3755-Hanbang_Zhan_U-O_NRSF/L3755-Hanbang_Zhan_U-O_NRSF.250413_NB551514_0281_AHHLNJBGXW.end1.fastq.gz,L3755-Hanbang_Zhan_U-O_NRSF.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3755-Hanbang_Zhan_U-O_NRSF.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L3756-Hanbang_Zhan_B-HP_NRSF/L3756-Hanbang_Zhan_B-HP_NRSF.250413_NB551514_0281_AHHLNJBGXW.end1.fastq.gz,L3756-Hanbang_Zhan_B-HP_NRSF.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3756-Hanbang_Zhan_B-HP_NRSF.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L3757-Hanbang_Zhan_B-HP_NRSF/L3757-Hanbang_Zhan_B-HP_NRSF.250413_NB551514_0281_AHHLNJBGXW.end1.fastq.gz,L3757-Hanbang_Zhan_B-HP_NRSF.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3757-Hanbang_Zhan_B-HP_NRSF.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L3758-Hanbang_Zhan_B-O_NRSF/L3758-Hanbang_Zhan_B-O_NRSF.250413_NB551514_0281_AHHLNJBGXW.end1.fastq.gz,L3758-Hanbang_Zhan_B-O_NRSF.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3758-Hanbang_Zhan_B-O_NRSF.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L3759-Hanbang_Zhan_B-O_NRSF/L3759-Hanbang_Zhan_B-O_NRSF.250413_NB551514_0281_AHHLNJBGXW.end1.fastq.gz,L3759-Hanbang_Zhan_B-O_NRSF.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3759-Hanbang_Zhan_B-O_NRSF.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3905-K562_KLF1-PA5-86441.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3905-K562_KLF1-PA5-86441.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3906-Julia1_KLF1-PA5-86441.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3906-Julia1_KLF1-PA5-86441.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3907-K562_KLF1-NB100-1019.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3907-K562_KLF1-NB100-1019.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3908-Julia2_KLF1-NB100-1019.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3908-Julia2_KLF1-NB100-1019.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3909-Julia1_KLF1-H00010661.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3909-Julia1_KLF1-H00010661.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3910-Julia2_KLF1-H00010661.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3910-Julia2_KLF1-H00010661.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3915-K562_Input.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3915-K562_Input.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3916-Mkay_WT-1.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3916-Mkay_WT-1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3917-Mkay_WT-2.250617_NB551514_0308_AH3YLNBGYX.end1.fastq.gz 36 -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-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3917-Mkay_WT-2.1x36mers.unique