python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_ATACseq-GSM3677739.end1.fastq.gz 2d_ATACseq-GSM3677739.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_ATACseq-GSM3677739.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_CTCF_auto-GSM3677740.end1.fastq.gz 2d_CTCF_auto-GSM3677740.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_CTCF_auto-GSM3677740.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_CTCF_hiCa-GSM3677741.end1.fastq.gz 2d_CTCF_hiCa-GSM3677741.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_CTCF_hiCa-GSM3677741.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_EOMES-GSM3677742.end1.fastq.gz 2d_EOMES-GSM3677742.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_EOMES-GSM3677742.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_FoxA1_auto-GSM3677743.end1.fastq.gz 2d_FoxA1_auto-GSM3677743.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_FoxA1_auto-GSM3677743.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_FoxA1_hiCa-GSM3677744.end1.fastq.gz 2d_FoxA1_hiCa-GSM3677744.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_FoxA1_hiCa-GSM3677744.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_FoxA1_std-GSM3677745.end1.fastq.gz 2d_FoxA1_std-GSM3677745.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_FoxA1_std-GSM3677745.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_FoxA2_auto-GSM3677746.end1.fastq.gz 2d_FoxA2_auto-GSM3677746.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_FoxA2_auto-GSM3677746.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_FoxA2_hiCa-GSM3677747.end1.fastq.gz 2d_FoxA2_hiCa-GSM3677747.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_FoxA2_hiCa-GSM3677747.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_GATA4-GSM3677748.end1.fastq.gz 2d_GATA4-GSM3677748.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_GATA4-GSM3677748.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_H3K27ac-GSM3677749.end1.fastq.gz 2d_H3K27ac-GSM3677749.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_H3K27ac-GSM3677749.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_H3K27me3-GSM3677750.end1.fastq.gz 2d_H3K27me3-GSM3677750.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_H3K27me3-GSM3677750.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_H3K4me2-GSM3677751.end1.fastq.gz 2d_H3K4me2-GSM3677751.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_H3K4me2-GSM3677751.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_IgG_A_auto-GSM3677752.end1.fastq.gz 2d_IgG_A_auto-GSM3677752.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_IgG_A_auto-GSM3677752.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_IgG_B_auto-GSM3677753.end1.fastq.gz 2d_IgG_B_auto-GSM3677753.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_IgG_B_auto-GSM3677753.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_IgG_std-GSM3677754.end1.fastq.gz 2d_IgG_std-GSM3677754.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_IgG_std-GSM3677754.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_Nanog-GSM3677755.end1.fastq.gz 2d_Nanog-GSM3677755.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_Nanog-GSM3677755.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_POU5F1_hiCa-GSM3677756.end1.fastq.gz 2d_POU5F1_hiCa-GSM3677756.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_POU5F1_hiCa-GSM3677756.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_POU5F1_std-GSM3677757.end1.fastq.gz 2d_POU5F1_std-GSM3677757.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_POU5F1_std-GSM3677757.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_Sox17-GSM3677758.end1.fastq.gz 2d_Sox17-GSM3677758.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_Sox17-GSM3677758.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_Sox2-GSM3677759.end1.fastq.gz 2d_Sox2-GSM3677759.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_Sox2-GSM3677759.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2d_T-GSM3677760.end1.fastq.gz 2d_T-GSM3677760.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2d_T-GSM3677760.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_ATACseq-GSM3677761.end1.fastq.gz 3d_ATACseq-GSM3677761.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_ATACseq-GSM3677761.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_CTCF_auto-GSM3677762.end1.fastq.gz 3d_CTCF_auto-GSM3677762.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_CTCF_auto-GSM3677762.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_CTCF_hiCa-GSM3677763.end1.fastq.gz 3d_CTCF_hiCa-GSM3677763.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_CTCF_hiCa-GSM3677763.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_EOMES-GSM3677764.end1.fastq.gz 3d_EOMES-GSM3677764.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_EOMES-GSM3677764.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_FoxA1_auto-GSM3677765.end1.fastq.gz 3d_FoxA1_auto-GSM3677765.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_FoxA1_auto-GSM3677765.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_FoxA1_hiCa-GSM3677766.end1.fastq.gz 3d_FoxA1_hiCa-GSM3677766.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_FoxA1_hiCa-GSM3677766.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_FoxA1_std-GSM3677767.end1.fastq.gz 3d_FoxA1_std-GSM3677767.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_FoxA1_std-GSM3677767.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_FoxA2_auto-GSM3677768.end1.fastq.gz 3d_FoxA2_auto-GSM3677768.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_FoxA2_auto-GSM3677768.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_FoxA2_hiCa-GSM3677769.end1.fastq.gz 3d_FoxA2_hiCa-GSM3677769.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_FoxA2_hiCa-GSM3677769.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_GATA4-GSM3677770.end1.fastq.gz 3d_GATA4-GSM3677770.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_GATA4-GSM3677770.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_H3K27ac-GSM3677771.end1.fastq.gz 3d_H3K27ac-GSM3677771.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_H3K27ac-GSM3677771.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_H3K27me3-GSM3677772.end1.fastq.gz 3d_H3K27me3-GSM3677772.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_H3K27me3-GSM3677772.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_H3K4me2-GSM3677773.end1.fastq.gz 3d_H3K4me2-GSM3677773.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_H3K4me2-GSM3677773.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_IgG_A_auto-GSM3677774.end1.fastq.gz 3d_IgG_A_auto-GSM3677774.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_IgG_A_auto-GSM3677774.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_IgG_B_auto-GSM3677775.end1.fastq.gz 3d_IgG_B_auto-GSM3677775.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_IgG_B_auto-GSM3677775.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_IgG_std-GSM3677776.end1.fastq.gz 3d_IgG_std-GSM3677776.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_IgG_std-GSM3677776.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_Nanog-GSM3677777.end1.fastq.gz 3d_Nanog-GSM3677777.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_Nanog-GSM3677777.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_POU5F1_hiCa-GSM3677778.end1.fastq.gz 3d_POU5F1_hiCa-GSM3677778.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_POU5F1_hiCa-GSM3677778.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_POU5F1_std-GSM3677779.end1.fastq.gz 3d_POU5F1_std-GSM3677779.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_POU5F1_std-GSM3677779.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_Sox17-GSM3677780.end1.fastq.gz 3d_Sox17-GSM3677780.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_Sox17-GSM3677780.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_Sox2-GSM3677781.end1.fastq.gz 3d_Sox2-GSM3677781.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_Sox2-GSM3677781.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3d_T-GSM3677782.end1.fastq.gz 3d_T-GSM3677782.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3d_T-GSM3677782.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_ATACseq-GSM3677783.end1.fastq.gz 4d_ATACseq-GSM3677783.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_ATACseq-GSM3677783.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_CTCF_auto-GSM3677784.end1.fastq.gz 4d_CTCF_auto-GSM3677784.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_CTCF_auto-GSM3677784.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_CTCF_hiCa-GSM3677785.end1.fastq.gz 4d_CTCF_hiCa-GSM3677785.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_CTCF_hiCa-GSM3677785.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_EOMES-GSM3677786.end1.fastq.gz 4d_EOMES-GSM3677786.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_EOMES-GSM3677786.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_FoxA1_auto-GSM3677787.end1.fastq.gz 4d_FoxA1_auto-GSM3677787.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_FoxA1_auto-GSM3677787.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_FoxA1_hiCa-GSM3677788.end1.fastq.gz 4d_FoxA1_hiCa-GSM3677788.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_FoxA1_hiCa-GSM3677788.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_FoxA1_std-GSM3677789.end1.fastq.gz 4d_FoxA1_std-GSM3677789.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_FoxA1_std-GSM3677789.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_FoxA2_auto-GSM3677790.end1.fastq.gz 4d_FoxA2_auto-GSM3677790.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_FoxA2_auto-GSM3677790.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_FoxA2_hiCa-GSM3677791.end1.fastq.gz 4d_FoxA2_hiCa-GSM3677791.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_FoxA2_hiCa-GSM3677791.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_GATA4-GSM3677792.end1.fastq.gz 4d_GATA4-GSM3677792.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_GATA4-GSM3677792.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_H3K27ac-GSM3677793.end1.fastq.gz 4d_H3K27ac-GSM3677793.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_H3K27ac-GSM3677793.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_H3K27me3-GSM3677794.end1.fastq.gz 4d_H3K27me3-GSM3677794.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_H3K27me3-GSM3677794.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_H3K4me2-GSM3677795.end1.fastq.gz 4d_H3K4me2-GSM3677795.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_H3K4me2-GSM3677795.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_IgG_A_auto-GSM3677796.end1.fastq.gz 4d_IgG_A_auto-GSM3677796.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_IgG_A_auto-GSM3677796.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_IgG_B_auto-GSM3677797.end1.fastq.gz 4d_IgG_B_auto-GSM3677797.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_IgG_B_auto-GSM3677797.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_IgG_std-GSM3677798.end1.fastq.gz 4d_IgG_std-GSM3677798.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_IgG_std-GSM3677798.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_Nanog-GSM3677799.end1.fastq.gz 4d_Nanog-GSM3677799.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_Nanog-GSM3677799.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_POU5F1_hiCa-GSM3677800.end1.fastq.gz 4d_POU5F1_hiCa-GSM3677800.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_POU5F1_hiCa-GSM3677800.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_POU5F1_std-GSM3677801.end1.fastq.gz 4d_POU5F1_std-GSM3677801.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_POU5F1_std-GSM3677801.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_Sox17-GSM3677802.end1.fastq.gz 4d_Sox17-GSM3677802.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_Sox17-GSM3677802.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_Sox2-GSM3677803.end1.fastq.gz 4d_Sox2-GSM3677803.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_Sox2-GSM3677803.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4d_T-GSM3677804.end1.fastq.gz 4d_T-GSM3677804.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4d_T-GSM3677804.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_ATACseq-GSM3677805.end1.fastq.gz DE_ATACseq-GSM3677805.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_ATACseq-GSM3677805.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_CTCF_auto-GSM3677806.end1.fastq.gz DE_CTCF_auto-GSM3677806.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_CTCF_auto-GSM3677806.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_CTCF_hiCa-GSM3677807.end1.fastq.gz DE_CTCF_hiCa-GSM3677807.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_CTCF_hiCa-GSM3677807.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_EOMES-GSM3677808.end1.fastq.gz DE_EOMES-GSM3677808.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_EOMES-GSM3677808.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_FoxA1_auto-GSM3677809.end1.fastq.gz DE_FoxA1_auto-GSM3677809.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_FoxA1_auto-GSM3677809.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_FoxA1_hiCa-GSM3677810.end1.fastq.gz DE_FoxA1_hiCa-GSM3677810.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_FoxA1_hiCa-GSM3677810.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_FoxA2_auto-GSM3677811.end1.fastq.gz DE_FoxA2_auto-GSM3677811.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_FoxA2_auto-GSM3677811.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_FoxA2_hiCa-GSM3677812.end1.fastq.gz DE_FoxA2_hiCa-GSM3677812.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_FoxA2_hiCa-GSM3677812.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_GATA4-GSM3677813.end1.fastq.gz DE_GATA4-GSM3677813.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_GATA4-GSM3677813.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_H3K27ac-GSM3677814.end1.fastq.gz DE_H3K27ac-GSM3677814.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_H3K27ac-GSM3677814.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_H3K27me3-GSM3677815.end1.fastq.gz DE_H3K27me3-GSM3677815.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_H3K27me3-GSM3677815.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_H3K4me2-GSM3677816.end1.fastq.gz DE_H3K4me2-GSM3677816.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_H3K4me2-GSM3677816.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_IgG_A_auto-GSM3677817.end1.fastq.gz DE_IgG_A_auto-GSM3677817.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_IgG_A_auto-GSM3677817.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_IgG_B_auto-GSM3677818.end1.fastq.gz DE_IgG_B_auto-GSM3677818.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_IgG_B_auto-GSM3677818.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_Nanog-GSM3677819.end1.fastq.gz DE_Nanog-GSM3677819.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_Nanog-GSM3677819.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_POU5F1-GSM3677820.end1.fastq.gz DE_POU5F1-GSM3677820.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_POU5F1-GSM3677820.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_Sox17-GSM3677821.end1.fastq.gz DE_Sox17-GSM3677821.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_Sox17-GSM3677821.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py DE_Sox2-GSM3677822.end1.fastq.gz DE_Sox2-GSM3677822.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - DE_Sox2-GSM3677822.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_ATACseq-GSM3677823.end1.fastq.gz H1_ATACseq-GSM3677823.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_ATACseq-GSM3677823.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_CTCF-GSM3677824.end1.fastq.gz H1_CTCF-GSM3677824.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_CTCF-GSM3677824.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_EOMES-GSM3677825.end1.fastq.gz H1_EOMES-GSM3677825.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_EOMES-GSM3677825.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_FoxA1_auto-GSM3677826.end1.fastq.gz H1_FoxA1_auto-GSM3677826.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_FoxA1_auto-GSM3677826.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_FoxA1_std-GSM3677827.end1.fastq.gz H1_FoxA1_std-GSM3677827.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_FoxA1_std-GSM3677827.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_FoxA2_auto-GSM3677828.end1.fastq.gz H1_FoxA2_auto-GSM3677828.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_FoxA2_auto-GSM3677828.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_FoxA2_hiCa-GSM3677829.end1.fastq.gz H1_FoxA2_hiCa-GSM3677829.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_FoxA2_hiCa-GSM3677829.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_GATA4-GSM3677830.end1.fastq.gz H1_GATA4-GSM3677830.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_GATA4-GSM3677830.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_H3.3-GSM3677831.end1.fastq.gz H1_H3.3-GSM3677831.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_H3.3-GSM3677831.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_H3K27ac-GSM3677832.end1.fastq.gz H1_H3K27ac-GSM3677832.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_H3K27ac-GSM3677832.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_H3K27me3-GSM3677833.end1.fastq.gz H1_H3K27me3-GSM3677833.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_H3K27me3-GSM3677833.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_H3K4me2-GSM3677834.end1.fastq.gz H1_H3K4me2-GSM3677834.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_H3K4me2-GSM3677834.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_IgG_A_auto-GSM3677835.end1.fastq.gz H1_IgG_A_auto-GSM3677835.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_IgG_A_auto-GSM3677835.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_IgG_B_auto-GSM3677836.end1.fastq.gz H1_IgG_B_auto-GSM3677836.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_IgG_B_auto-GSM3677836.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_IgG_std-GSM3677837.end1.fastq.gz H1_IgG_std-GSM3677837.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_IgG_std-GSM3677837.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_Nanog-GSM3677838.end1.fastq.gz H1_Nanog-GSM3677838.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_Nanog-GSM3677838.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_POU5F1_hiCa-GSM3677839.end1.fastq.gz H1_POU5F1_hiCa-GSM3677839.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_POU5F1_hiCa-GSM3677839.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_POU5F1_std-GSM3677840.end1.fastq.gz H1_POU5F1_std-GSM3677840.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_POU5F1_std-GSM3677840.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_SUZ12-GSM3677844.end1.fastq.gz H1_SUZ12-GSM3677844.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_SUZ12-GSM3677844.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_Sox17-GSM3677841.end1.fastq.gz H1_Sox17-GSM3677841.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_Sox17-GSM3677841.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_Sox2_auto-GSM3677842.end1.fastq.gz H1_Sox2_auto-GSM3677842.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_Sox2_auto-GSM3677842.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_Sox2_std-GSM3677843.end1.fastq.gz H1_Sox2_std-GSM3677843.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_Sox2_std-GSM3677843.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py H1_T-GSM3677845.end1.fastq.gz H1_T-GSM3677845.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H1_T-GSM3677845.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py K562_Max-GSM3677846.end1.fastq.gz K562_Max-GSM3677846.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562_Max-GSM3677846.2x25mers.hg38-no_haps.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py K562_Myc-GSM3677847.end1.fastq.gz K562_Myc-GSM3677847.end2.fastq.gz -trim 25 25 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -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/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562_Myc-GSM3677847.2x25mers.hg38-no_haps.unique