python ~/code/PEFastqToTabDelimited.py Ace2_ChIP_rep1-GSM8445821/SRR30166721_1.fastq Ace2_ChIP_rep1-GSM8445821/SRR30166721_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ace2_ChIP_rep1-GSM8445821.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ace2_ChIP_rep2-GSM8445822/SRR30166720_1.fastq Ace2_ChIP_rep2-GSM8445822/SRR30166720_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ace2_ChIP_rep2-GSM8445822.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ace2_IN_rep1-GSM8445819/SRR30166723_1.fastq Ace2_IN_rep1-GSM8445819/SRR30166723_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ace2_IN_rep1-GSM8445819.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ace2_IN_rep2-GSM8445820/SRR30166722_1.fastq Ace2_IN_rep2-GSM8445820/SRR30166722_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ace2_IN_rep2-GSM8445820.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Adn2_ChIP_rep1-GSM8445857/SRR30166701_1.fastq Adn2_ChIP_rep1-GSM8445857/SRR30166701_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Adn2_ChIP_rep1-GSM8445857.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Adn2_ChIP_rep2-GSM8445858/SRR30166700_1.fastq Adn2_ChIP_rep2-GSM8445858/SRR30166700_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Adn2_ChIP_rep2-GSM8445858.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Adn2_IN_rep1-GSM8445855/SRR30166703_1.fastq Adn2_IN_rep1-GSM8445855/SRR30166703_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Adn2_IN_rep1-GSM8445855.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Adn2_IN_rep2-GSM8445856/SRR30166702_1.fastq Adn2_IN_rep2-GSM8445856/SRR30166702_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Adn2_IN_rep2-GSM8445856.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Adn3_ChIP_rep1-GSM8445869/SRR30166689_1.fastq Adn3_ChIP_rep1-GSM8445869/SRR30166689_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Adn3_ChIP_rep1-GSM8445869.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Adn3_ChIP_rep2-GSM8445870/SRR30166688_1.fastq Adn3_ChIP_rep2-GSM8445870/SRR30166688_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Adn3_ChIP_rep2-GSM8445870.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Adn3_IN_rep1-GSM8445867/SRR30166691_1.fastq Adn3_IN_rep1-GSM8445867/SRR30166691_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Adn3_IN_rep1-GSM8445867.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Adn3_IN_rep2-GSM8445868/SRR30166690_1.fastq Adn3_IN_rep2-GSM8445868/SRR30166690_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Adn3_IN_rep2-GSM8445868.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ams2_ChIP_rep1-GSM8445873/SRR30166685_1.fastq Ams2_ChIP_rep1-GSM8445873/SRR30166685_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ams2_ChIP_rep1-GSM8445873.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ams2_ChIP_rep2-GSM8445874/SRR30166684_1.fastq Ams2_ChIP_rep2-GSM8445874/SRR30166684_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ams2_ChIP_rep2-GSM8445874.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ams2_IN_rep1-GSM8445871/SRR30166687_1.fastq Ams2_IN_rep1-GSM8445871/SRR30166687_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ams2_IN_rep1-GSM8445871.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ams2_IN_rep2-GSM8445872/SRR30166686_1.fastq Ams2_IN_rep2-GSM8445872/SRR30166686_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ams2_IN_rep2-GSM8445872.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Atf1_ChIP_rep1-GSM8445881/SRR30166677_1.fastq Atf1_ChIP_rep1-GSM8445881/SRR30166677_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Atf1_ChIP_rep1-GSM8445881.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Atf1_ChIP_rep2-GSM8445882/SRR30166676_1.fastq Atf1_ChIP_rep2-GSM8445882/SRR30166676_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Atf1_ChIP_rep2-GSM8445882.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Atf1_IN_rep1-GSM8445879/SRR30166679_1.fastq Atf1_IN_rep1-GSM8445879/SRR30166679_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Atf1_IN_rep1-GSM8445879.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Atf1_IN_rep2-GSM8445880/SRR30166678_1.fastq Atf1_IN_rep2-GSM8445880/SRR30166678_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Atf1_IN_rep2-GSM8445880.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Cbf11_ChIP_rep1-GSM8445897/SRR30166677_1.fastq Cbf11_ChIP_rep1-GSM8445897/SRR30166677_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cbf11_ChIP_rep1-GSM8445897.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Cbf11_ChIP_rep2-GSM8445898/SRR30166676_1.fastq Cbf11_ChIP_rep2-GSM8445898/SRR30166676_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cbf11_ChIP_rep2-GSM8445898.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Cbf11_IN_rep1-GSM8445895/SRR30166679_1.fastq Cbf11_IN_rep1-GSM8445895/SRR30166679_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cbf11_IN_rep1-GSM8445895.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Cbf11_IN_rep2-GSM8445896/SRR30166678_1.fastq Cbf11_IN_rep2-GSM8445896/SRR30166678_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cbf11_IN_rep2-GSM8445896.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Cdc10_ChIP_rep1-GSM8445825/SRR30166717_1.fastq Cdc10_ChIP_rep1-GSM8445825/SRR30166717_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cdc10_ChIP_rep1-GSM8445825.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Cdc10_ChIP_rep2-GSM8445826/SRR30166716_1.fastq Cdc10_ChIP_rep2-GSM8445826/SRR30166716_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cdc10_ChIP_rep2-GSM8445826.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Cdc10_IN_rep1-GSM8445823/SRR30166719_1.fastq Cdc10_IN_rep1-GSM8445823/SRR30166719_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cdc10_IN_rep1-GSM8445823.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Cdc10_IN_rep2-GSM8445824/SRR30166718_1.fastq Cdc10_IN_rep2-GSM8445824/SRR30166718_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cdc10_IN_rep2-GSM8445824.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Cuf1_ChIP_rep1-GSM8445829/SRR30166713_1.fastq Cuf1_ChIP_rep1-GSM8445829/SRR30166713_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cuf1_ChIP_rep1-GSM8445829.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Cuf1_ChIP_rep2-GSM8445830/SRR30166712_1.fastq Cuf1_ChIP_rep2-GSM8445830/SRR30166712_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cuf1_ChIP_rep2-GSM8445830.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Cuf1_IN_rep1-GSM8445827/SRR30166715_1.fastq Cuf1_IN_rep1-GSM8445827/SRR30166715_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cuf1_IN_rep1-GSM8445827.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Cuf1_IN_rep2-GSM8445828/SRR30166714_1.fastq Cuf1_IN_rep2-GSM8445828/SRR30166714_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cuf1_IN_rep2-GSM8445828.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Dal81_ChIP_rep1-GSM8446049/SRR30166589_1.fastq Dal81_ChIP_rep1-GSM8446049/SRR30166589_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Dal81_ChIP_rep1-GSM8446049.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Dal81_ChIP_rep2-GSM8446050/SRR30166588_1.fastq Dal81_ChIP_rep2-GSM8446050/SRR30166588_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Dal81_ChIP_rep2-GSM8446050.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Dal81_IN_rep1-GSM8446047/SRR30166591_1.fastq Dal81_IN_rep1-GSM8446047/SRR30166591_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Dal81_IN_rep1-GSM8446047.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Dal81_IN_rep2-GSM8446048/SRR30166590_1.fastq Dal81_IN_rep2-GSM8446048/SRR30166590_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Dal81_IN_rep2-GSM8446048.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Deb1_ChIP_rep1-GSM8445833/SRR30166709_1.fastq Deb1_ChIP_rep1-GSM8445833/SRR30166709_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Deb1_ChIP_rep1-GSM8445833.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Deb1_ChIP_rep2-GSM8445834/SRR30166708_1.fastq Deb1_ChIP_rep2-GSM8445834/SRR30166708_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Deb1_ChIP_rep2-GSM8445834.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Deb1_IN_rep1-GSM8445831/SRR30166711_1.fastq Deb1_IN_rep1-GSM8445831/SRR30166711_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Deb1_IN_rep1-GSM8445831.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Deb1_IN_rep2-GSM8445832/SRR30166710_1.fastq Deb1_IN_rep2-GSM8445832/SRR30166710_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Deb1_IN_rep2-GSM8445832.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Esc1_ChIP_rep1-GSM8445837/SRR30166625_1.fastq Esc1_ChIP_rep1-GSM8445837/SRR30166625_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Esc1_ChIP_rep1-GSM8445837.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Esc1_ChIP_rep2-GSM8445838/SRR30166624_1.fastq Esc1_ChIP_rep2-GSM8445838/SRR30166624_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Esc1_ChIP_rep2-GSM8445838.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Esc1_IN_rep1-GSM8445835/SRR30166627_1.fastq Esc1_IN_rep1-GSM8445835/SRR30166627_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Esc1_IN_rep1-GSM8445835.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Esc1_IN_rep2-GSM8445836/SRR30166626_1.fastq Esc1_IN_rep2-GSM8445836/SRR30166626_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Esc1_IN_rep2-GSM8445836.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fep1_ChIP_rep1-GSM8445841/SRR30166621_1.fastq Fep1_ChIP_rep1-GSM8445841/SRR30166621_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fep1_ChIP_rep1-GSM8445841.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fep1_ChIP_rep2-GSM8445842/SRR30166620_1.fastq Fep1_ChIP_rep2-GSM8445842/SRR30166620_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fep1_ChIP_rep2-GSM8445842.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fep1_IN_rep1-GSM8445839/SRR30166623_1.fastq Fep1_IN_rep1-GSM8445839/SRR30166623_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fep1_IN_rep1-GSM8445839.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fep1_IN_rep2-GSM8445840/SRR30166622_1.fastq Fep1_IN_rep2-GSM8445840/SRR30166622_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fep1_IN_rep2-GSM8445840.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fhl1_ChIP_rep1-GSM8445845/SRR30166617_1.fastq Fhl1_ChIP_rep1-GSM8445845/SRR30166617_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fhl1_ChIP_rep1-GSM8445845.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fhl1_ChIP_rep2-GSM8445846/SRR30166616_1.fastq Fhl1_ChIP_rep2-GSM8445846/SRR30166616_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fhl1_ChIP_rep2-GSM8445846.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fhl1_IN_rep1-GSM8445843/SRR30166619_1.fastq Fhl1_IN_rep1-GSM8445843/SRR30166619_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fhl1_IN_rep1-GSM8445843.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fhl1_IN_rep2-GSM8445844/SRR30166618_1.fastq Fhl1_IN_rep2-GSM8445844/SRR30166618_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fhl1_IN_rep2-GSM8445844.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fil1_ChIP_rep1-GSM8445849/SRR30166613_1.fastq Fil1_ChIP_rep1-GSM8445849/SRR30166613_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fil1_ChIP_rep1-GSM8445849.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fil1_ChIP_rep2-GSM8445850/SRR30166612_1.fastq Fil1_ChIP_rep2-GSM8445850/SRR30166612_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fil1_ChIP_rep2-GSM8445850.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fil1_IN_rep1-GSM8445847/SRR30166615_1.fastq Fil1_IN_rep1-GSM8445847/SRR30166615_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fil1_IN_rep1-GSM8445847.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fil1_IN_rep2-GSM8445848/SRR30166614_1.fastq Fil1_IN_rep2-GSM8445848/SRR30166614_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fil1_IN_rep2-GSM8445848.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fkh2_ChIP_rep1-GSM8445853/SRR30166705_1.fastq Fkh2_ChIP_rep1-GSM8445853/SRR30166705_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fkh2_ChIP_rep1-GSM8445853.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fkh2_ChIP_rep2-GSM8445854/SRR30166704_1.fastq Fkh2_ChIP_rep2-GSM8445854/SRR30166704_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fkh2_ChIP_rep2-GSM8445854.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fkh2_IN_rep1-GSM8445851/SRR30166707_1.fastq Fkh2_IN_rep1-GSM8445851/SRR30166707_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fkh2_IN_rep1-GSM8445851.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Fkh2_IN_rep2-GSM8445852/SRR30166706_1.fastq Fkh2_IN_rep2-GSM8445852/SRR30166706_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fkh2_IN_rep2-GSM8445852.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Gaf1_ChIP_rep1-GSM8445861/SRR30166697_1.fastq Gaf1_ChIP_rep1-GSM8445861/SRR30166697_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Gaf1_ChIP_rep1-GSM8445861.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Gaf1_ChIP_rep2-GSM8445862/SRR30166696_1.fastq Gaf1_ChIP_rep2-GSM8445862/SRR30166696_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Gaf1_ChIP_rep2-GSM8445862.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Gaf1_IN_rep1-GSM8445859/SRR30166699_1.fastq Gaf1_IN_rep1-GSM8445859/SRR30166699_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Gaf1_IN_rep1-GSM8445859.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Gaf1_IN_rep2-GSM8445860/SRR30166698_1.fastq Gaf1_IN_rep2-GSM8445860/SRR30166698_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Gaf1_IN_rep2-GSM8445860.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Grt1_ChIP_rep1-GSM8445997/SRR30166778_1.fastq Grt1_ChIP_rep1-GSM8445997/SRR30166778_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Grt1_ChIP_rep1-GSM8445997.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Grt1_ChIP_rep2-GSM8445998/SRR30166777_1.fastq Grt1_ChIP_rep2-GSM8445998/SRR30166777_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Grt1_ChIP_rep2-GSM8445998.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Grt1_IN_rep1-GSM8445995/SRR30166828_1.fastq Grt1_IN_rep1-GSM8445995/SRR30166828_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Grt1_IN_rep1-GSM8445995.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Grt1_IN_rep2-GSM8445996/SRR30166779_1.fastq Grt1_IN_rep2-GSM8445996/SRR30166779_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Grt1_IN_rep2-GSM8445996.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Gsf1_ChIP_rep1-GSM8446001/SRR30166774_1.fastq Gsf1_ChIP_rep1-GSM8446001/SRR30166774_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Gsf1_ChIP_rep1-GSM8446001.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Gsf1_ChIP_rep2-GSM8446002/SRR30166773_1.fastq Gsf1_ChIP_rep2-GSM8446002/SRR30166773_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Gsf1_ChIP_rep2-GSM8446002.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Gsf1_IN_rep1-GSM8445999/SRR30166776_1.fastq Gsf1_IN_rep1-GSM8445999/SRR30166776_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Gsf1_IN_rep1-GSM8445999.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Gsf1_IN_rep2-GSM8446000/SRR30166775_1.fastq Gsf1_IN_rep2-GSM8446000/SRR30166775_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Gsf1_IN_rep2-GSM8446000.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Hsf1_ChIP_rep1-GSM8445865/SRR30166693_1.fastq Hsf1_ChIP_rep1-GSM8445865/SRR30166693_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Hsf1_ChIP_rep1-GSM8445865.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Hsf1_ChIP_rep2-GSM8445866/SRR30166692_1.fastq Hsf1_ChIP_rep2-GSM8445866/SRR30166692_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Hsf1_ChIP_rep2-GSM8445866.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Hsf1_IN_rep1-GSM8445863/SRR30166695_1.fastq Hsf1_IN_rep1-GSM8445863/SRR30166695_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Hsf1_IN_rep1-GSM8445863.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Hsf1_IN_rep2-GSM8445864/SRR30166694_1.fastq Hsf1_IN_rep2-GSM8445864/SRR30166694_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Hsf1_IN_rep2-GSM8445864.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Hsr1_ChIP_rep1-GSM8445993/SRR30166830_1.fastq Hsr1_ChIP_rep1-GSM8445993/SRR30166830_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Hsr1_ChIP_rep1-GSM8445993.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Hsr1_ChIP_rep2-GSM8445994/SRR30166829_1.fastq Hsr1_ChIP_rep2-GSM8445994/SRR30166829_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Hsr1_ChIP_rep2-GSM8445994.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Hsr1_IN_rep1-GSM8445991/SRR30166832_1.fastq Hsr1_IN_rep1-GSM8445991/SRR30166832_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Hsr1_IN_rep1-GSM8445991.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Hsr1_IN_rep2-GSM8445992/SRR30166831_1.fastq Hsr1_IN_rep2-GSM8445992/SRR30166831_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Hsr1_IN_rep2-GSM8445992.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Klf1_ChIP_rep1-GSM8446005/SRR30166770_1.fastq Klf1_ChIP_rep1-GSM8446005/SRR30166770_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Klf1_ChIP_rep1-GSM8446005.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Klf1_ChIP_rep2-GSM8446006/SRR30166769_1.fastq Klf1_ChIP_rep2-GSM8446006/SRR30166769_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Klf1_ChIP_rep2-GSM8446006.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Klf1_IN_rep1-GSM8446003/SRR30166772_1.fastq Klf1_IN_rep1-GSM8446003/SRR30166772_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Klf1_IN_rep1-GSM8446003.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Klf1_IN_rep2-GSM8446004/SRR30166771_1.fastq Klf1_IN_rep2-GSM8446004/SRR30166771_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Klf1_IN_rep2-GSM8446004.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Loz1_ChIP_rep1-GSM8445901/SRR30166673_1.fastq Loz1_ChIP_rep1-GSM8445901/SRR30166673_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Loz1_ChIP_rep1-GSM8445901.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Loz1_ChIP_rep2-GSM8445902/SRR30166672_1.fastq Loz1_ChIP_rep2-GSM8445902/SRR30166672_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Loz1_ChIP_rep2-GSM8445902.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Loz1_IN_rep1-GSM8445899/SRR30166675_1.fastq Loz1_IN_rep1-GSM8445899/SRR30166675_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Loz1_IN_rep1-GSM8445899.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Loz1_IN_rep2-GSM8445900/SRR30166674_1.fastq Loz1_IN_rep2-GSM8445900/SRR30166674_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Loz1_IN_rep2-GSM8445900.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Map1_ChIP_rep1-GSM8445905/SRR30166669_1.fastq Map1_ChIP_rep1-GSM8445905/SRR30166669_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Map1_ChIP_rep1-GSM8445905.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Map1_ChIP_rep2-GSM8445906/SRR30166668_1.fastq Map1_ChIP_rep2-GSM8445906/SRR30166668_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Map1_ChIP_rep2-GSM8445906.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Map1_IN_rep1-GSM8445903/SRR30166671_1.fastq Map1_IN_rep1-GSM8445903/SRR30166671_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Map1_IN_rep1-GSM8445903.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Map1_IN_rep2-GSM8445904/SRR30166670_1.fastq Map1_IN_rep2-GSM8445904/SRR30166670_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Map1_IN_rep2-GSM8445904.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Mbx1_ChIP_rep1-GSM8445909/SRR30166665_1.fastq Mbx1_ChIP_rep1-GSM8445909/SRR30166665_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mbx1_ChIP_rep1-GSM8445909.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Mbx1_ChIP_rep2-GSM8445910/SRR30166664_1.fastq Mbx1_ChIP_rep2-GSM8445910/SRR30166664_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mbx1_ChIP_rep2-GSM8445910.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Mbx1_IN_rep1-GSM8445907/SRR30166667_1.fastq Mbx1_IN_rep1-GSM8445907/SRR30166667_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mbx1_IN_rep1-GSM8445907.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Mbx1_IN_rep2-GSM8445908/SRR30166666_1.fastq Mbx1_IN_rep2-GSM8445908/SRR30166666_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mbx1_IN_rep2-GSM8445908.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Mbx2_ChIP_rep1-GSM8445913/SRR30166661_1.fastq Mbx2_ChIP_rep1-GSM8445913/SRR30166661_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mbx2_ChIP_rep1-GSM8445913.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Mbx2_ChIP_rep2-GSM8445914/SRR30166660_1.fastq Mbx2_ChIP_rep2-GSM8445914/SRR30166660_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mbx2_ChIP_rep2-GSM8445914.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Mbx2_IN_rep1-GSM8445911/SRR30166663_1.fastq Mbx2_IN_rep1-GSM8445911/SRR30166663_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mbx2_IN_rep1-GSM8445911.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Mbx2_IN_rep2-GSM8445912/SRR30166662_1.fastq Mbx2_IN_rep2-GSM8445912/SRR30166662_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mbx2_IN_rep2-GSM8445912.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Mca1_ChIP_rep1-GSM8445917/SRR30166793_1.fastq Mca1_ChIP_rep1-GSM8445917/SRR30166793_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mca1_ChIP_rep1-GSM8445917.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Mca1_ChIP_rep2-GSM8445918/SRR30166792_1.fastq Mca1_ChIP_rep2-GSM8445918/SRR30166792_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mca1_ChIP_rep2-GSM8445918.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Mca1_IN_rep1-GSM8445915/SRR30166795_1.fastq Mca1_IN_rep1-GSM8445915/SRR30166795_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mca1_IN_rep1-GSM8445915.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Mca1_IN_rep2-GSM8445916/SRR30166794_1.fastq Mca1_IN_rep2-GSM8445916/SRR30166794_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mca1_IN_rep2-GSM8445916.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Moc3_ChIP_rep1-GSM8445921/SRR30166789_1.fastq Moc3_ChIP_rep1-GSM8445921/SRR30166789_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Moc3_ChIP_rep1-GSM8445921.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Moc3_ChIP_rep2-GSM8445922/SRR30166788_1.fastq Moc3_ChIP_rep2-GSM8445922/SRR30166788_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Moc3_ChIP_rep2-GSM8445922.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Moc3_IN_rep1-GSM8445919/SRR30166791_1.fastq Moc3_IN_rep1-GSM8445919/SRR30166791_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Moc3_IN_rep1-GSM8445919.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Moc3_IN_rep2-GSM8445920/SRR30166790_1.fastq Moc3_IN_rep2-GSM8445920/SRR30166790_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Moc3_IN_rep2-GSM8445920.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ntu1_ChIP_rep1-GSM8446089/SRR30166565_1.fastq Ntu1_ChIP_rep1-GSM8446089/SRR30166565_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ntu1_ChIP_rep1-GSM8446089.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ntu1_ChIP_rep2-GSM8446090/SRR30166564_1.fastq Ntu1_ChIP_rep2-GSM8446090/SRR30166564_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ntu1_ChIP_rep2-GSM8446090.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ntu1_IN_rep1-GSM8446087/SRR30166567_1.fastq Ntu1_IN_rep1-GSM8446087/SRR30166567_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ntu1_IN_rep1-GSM8446087.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ntu1_IN_rep2-GSM8446088/SRR30166566_1.fastq Ntu1_IN_rep2-GSM8446088/SRR30166566_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ntu1_IN_rep2-GSM8446088.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu1_KO_ntu2TAG_ChIP_rep1-GSM8446157/SRR30166729_1.fastq ntu1_KO_ntu2TAG_ChIP_rep1-GSM8446157/SRR30166729_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu1_KO_ntu2TAG_ChIP_rep1-GSM8446157.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu1_KO_ntu2TAG_ChIP_rep2-GSM8446158/SRR30166728_1.fastq ntu1_KO_ntu2TAG_ChIP_rep2-GSM8446158/SRR30166728_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu1_KO_ntu2TAG_ChIP_rep2-GSM8446158.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu1_KO_ntu2TAG_IN_rep1-GSM8446155/SRR30166731_1.fastq ntu1_KO_ntu2TAG_IN_rep1-GSM8446155/SRR30166731_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu1_KO_ntu2TAG_IN_rep1-GSM8446155.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu1_KO_ntu2TAG_IN_rep2-GSM8446156/SRR30166730_1.fastq ntu1_KO_ntu2TAG_IN_rep2-GSM8446156/SRR30166730_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu1_KO_ntu2TAG_IN_rep2-GSM8446156.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu1_TAG_ChIP_rep1-GSM8446145/SRR30166741_1.fastq ntu1_TAG_ChIP_rep1-GSM8446145/SRR30166741_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu1_TAG_ChIP_rep1-GSM8446145.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu1_TAG_ChIP_rep2-GSM8446146/SRR30166740_1.fastq ntu1_TAG_ChIP_rep2-GSM8446146/SRR30166740_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu1_TAG_ChIP_rep2-GSM8446146.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu1_TAG_IN_rep1-GSM8446143/SRR30166743_1.fastq ntu1_TAG_IN_rep1-GSM8446143/SRR30166743_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu1_TAG_IN_rep1-GSM8446143.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu1_TAG_IN_rep2-GSM8446144/SRR30166742_1.fastq ntu1_TAG_IN_rep2-GSM8446144/SRR30166742_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu1_TAG_IN_rep2-GSM8446144.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ntu2_ChIP_rep1-GSM8446105/SRR30166749_1.fastq Ntu2_ChIP_rep1-GSM8446105/SRR30166749_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ntu2_ChIP_rep1-GSM8446105.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ntu2_ChIP_rep2-GSM8446106/SRR30166748_1.fastq Ntu2_ChIP_rep2-GSM8446106/SRR30166748_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ntu2_ChIP_rep2-GSM8446106.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu2_delTMD_ChIP_rep1-GSM8446161/SRR30166725_1.fastq ntu2_delTMD_ChIP_rep1-GSM8446161/SRR30166725_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu2_delTMD_ChIP_rep1-GSM8446161.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu2_delTMD_ChIP_rep2-GSM8446162/SRR30166724_1.fastq ntu2_delTMD_ChIP_rep2-GSM8446162/SRR30166724_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu2_delTMD_ChIP_rep2-GSM8446162.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu2_delTMD_IN_rep1-GSM8446159/SRR30166727_1.fastq ntu2_delTMD_IN_rep1-GSM8446159/SRR30166727_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu2_delTMD_IN_rep1-GSM8446159.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu2_delTMD_IN_rep2-GSM8446160/SRR30166726_1.fastq ntu2_delTMD_IN_rep2-GSM8446160/SRR30166726_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu2_delTMD_IN_rep2-GSM8446160.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ntu2_IN_rep1-GSM8446103/SRR30166751_1.fastq Ntu2_IN_rep1-GSM8446103/SRR30166751_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ntu2_IN_rep1-GSM8446103.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ntu2_IN_rep2-GSM8446104/SRR30166750_1.fastq Ntu2_IN_rep2-GSM8446104/SRR30166750_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ntu2_IN_rep2-GSM8446104.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu2_KO_ntu1TAG_ChIP_rep1-GSM8446153/SRR30166733_1.fastq ntu2_KO_ntu1TAG_ChIP_rep1-GSM8446153/SRR30166733_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu2_KO_ntu1TAG_ChIP_rep1-GSM8446153.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu2_KO_ntu1TAG_ChIP_rep2-GSM8446154/SRR30166732_1.fastq ntu2_KO_ntu1TAG_ChIP_rep2-GSM8446154/SRR30166732_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu2_KO_ntu1TAG_ChIP_rep2-GSM8446154.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu2_KO_ntu1TAG_IN_rep1-GSM8446151/SRR30166735_1.fastq ntu2_KO_ntu1TAG_IN_rep1-GSM8446151/SRR30166735_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu2_KO_ntu1TAG_IN_rep1-GSM8446151.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu2_KO_ntu1TAG_IN_rep2-GSM8446152/SRR30166734_1.fastq ntu2_KO_ntu1TAG_IN_rep2-GSM8446152/SRR30166734_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu2_KO_ntu1TAG_IN_rep2-GSM8446152.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu2_TAG_ChIP_rep1-GSM8446149/SRR30166737_1.fastq ntu2_TAG_ChIP_rep1-GSM8446149/SRR30166737_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu2_TAG_ChIP_rep1-GSM8446149.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu2_TAG_ChIP_rep2-GSM8446150/SRR30166736_1.fastq ntu2_TAG_ChIP_rep2-GSM8446150/SRR30166736_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu2_TAG_ChIP_rep2-GSM8446150.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu2_TAG_IN_rep1-GSM8446147/SRR30166739_1.fastq ntu2_TAG_IN_rep1-GSM8446147/SRR30166739_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu2_TAG_IN_rep1-GSM8446147.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py ntu2_TAG_IN_rep2-GSM8446148/SRR30166738_1.fastq ntu2_TAG_IN_rep2-GSM8446148/SRR30166738_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ntu2_TAG_IN_rep2-GSM8446148.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Pap1_ChIP_rep1-GSM8445925/SRR30166785_1.fastq Pap1_ChIP_rep1-GSM8445925/SRR30166785_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Pap1_ChIP_rep1-GSM8445925.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Pap1_ChIP_rep2-GSM8445926/SRR30166784_1.fastq Pap1_ChIP_rep2-GSM8445926/SRR30166784_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Pap1_ChIP_rep2-GSM8445926.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Pap1_IN_rep1-GSM8445923/SRR30166787_1.fastq Pap1_IN_rep1-GSM8445923/SRR30166787_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Pap1_IN_rep1-GSM8445923.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Pap1_IN_rep2-GSM8445924/SRR30166786_1.fastq Pap1_IN_rep2-GSM8445924/SRR30166786_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Pap1_IN_rep2-GSM8445924.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Pcr1_ChIP_rep1-GSM8445929/SRR30166781_1.fastq Pcr1_ChIP_rep1-GSM8445929/SRR30166781_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Pcr1_ChIP_rep1-GSM8445929.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Pcr1_ChIP_rep2-GSM8445930/SRR30166780_1.fastq Pcr1_ChIP_rep2-GSM8445930/SRR30166780_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Pcr1_ChIP_rep2-GSM8445930.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Pcr1_IN_rep1-GSM8445927/SRR30166783_1.fastq Pcr1_IN_rep1-GSM8445927/SRR30166783_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Pcr1_IN_rep1-GSM8445927.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Pcr1_IN_rep2-GSM8445928/SRR30166782_1.fastq Pcr1_IN_rep2-GSM8445928/SRR30166782_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Pcr1_IN_rep2-GSM8445928.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Pho7_ChIP_rep1-GSM8445933/SRR30166857_1.fastq Pho7_ChIP_rep1-GSM8445933/SRR30166857_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Pho7_ChIP_rep1-GSM8445933.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Pho7_ChIP_rep2-GSM8445934/SRR30166856_1.fastq Pho7_ChIP_rep2-GSM8445934/SRR30166856_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Pho7_ChIP_rep2-GSM8445934.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Pho7_IN_rep1-GSM8445931/SRR30166859_1.fastq Pho7_IN_rep1-GSM8445931/SRR30166859_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Pho7_IN_rep1-GSM8445931.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Pho7_IN_rep2-GSM8445932/SRR30166858_1.fastq Pho7_IN_rep2-GSM8445932/SRR30166858_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Pho7_IN_rep2-GSM8445932.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Php2_ChIP_rep1-GSM8445937/SRR30166853_1.fastq Php2_ChIP_rep1-GSM8445937/SRR30166853_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Php2_ChIP_rep1-GSM8445937.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Php2_ChIP_rep2-GSM8445938/SRR30166852_1.fastq Php2_ChIP_rep2-GSM8445938/SRR30166852_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Php2_ChIP_rep2-GSM8445938.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Php2_IN_rep1-GSM8445935/SRR30166855_1.fastq Php2_IN_rep1-GSM8445935/SRR30166855_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Php2_IN_rep1-GSM8445935.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Php2_IN_rep2-GSM8445936/SRR30166854_1.fastq Php2_IN_rep2-GSM8445936/SRR30166854_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Php2_IN_rep2-GSM8445936.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Php3_ChIP_rep1-GSM8445941/SRR30166849_1.fastq Php3_ChIP_rep1-GSM8445941/SRR30166849_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Php3_ChIP_rep1-GSM8445941.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Php3_ChIP_rep2-GSM8445942/SRR30166848_1.fastq Php3_ChIP_rep2-GSM8445942/SRR30166848_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Php3_ChIP_rep2-GSM8445942.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Php3_IN_rep1-GSM8445939/SRR30166851_1.fastq Php3_IN_rep1-GSM8445939/SRR30166851_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Php3_IN_rep1-GSM8445939.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Php3_IN_rep2-GSM8445940/SRR30166850_1.fastq Php3_IN_rep2-GSM8445940/SRR30166850_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Php3_IN_rep2-GSM8445940.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Php5_ChIP_rep1-GSM8445945/SRR30166845_1.fastq Php5_ChIP_rep1-GSM8445945/SRR30166845_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Php5_ChIP_rep1-GSM8445945.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Php5_ChIP_rep2-GSM8445946/SRR30166844_1.fastq Php5_ChIP_rep2-GSM8445946/SRR30166844_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Php5_ChIP_rep2-GSM8445946.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Php5_IN_rep1-GSM8445943/SRR30166847_1.fastq Php5_IN_rep1-GSM8445943/SRR30166847_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Php5_IN_rep1-GSM8445943.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Php5_IN_rep2-GSM8445944/SRR30166846_1.fastq Php5_IN_rep2-GSM8445944/SRR30166846_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Php5_IN_rep2-GSM8445944.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Phx1_ChIP_rep1-GSM8445949/SRR30166609_1.fastq Phx1_ChIP_rep1-GSM8445949/SRR30166609_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Phx1_ChIP_rep1-GSM8445949.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Phx1_ChIP_rep2-GSM8445950/SRR30166608_1.fastq Phx1_ChIP_rep2-GSM8445950/SRR30166608_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Phx1_ChIP_rep2-GSM8445950.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Phx1_IN_rep1-GSM8445947/SRR30166611_1.fastq Phx1_IN_rep1-GSM8445947/SRR30166611_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Phx1_IN_rep1-GSM8445947.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Phx1_IN_rep2-GSM8445948/SRR30166610_1.fastq Phx1_IN_rep2-GSM8445948/SRR30166610_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Phx1_IN_rep2-GSM8445948.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Prr1_ChIP_rep1-GSM8445953/SRR30166605_1.fastq Prr1_ChIP_rep1-GSM8445953/SRR30166605_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Prr1_ChIP_rep1-GSM8445953.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Prr1_ChIP_rep2-GSM8445954/SRR30166604_1.fastq Prr1_ChIP_rep2-GSM8445954/SRR30166604_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Prr1_ChIP_rep2-GSM8445954.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Prr1_IN_rep1-GSM8445951/SRR30166607_1.fastq Prr1_IN_rep1-GSM8445951/SRR30166607_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Prr1_IN_rep1-GSM8445951.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Prr1_IN_rep2-GSM8445952/SRR30166606_1.fastq Prr1_IN_rep2-GSM8445952/SRR30166606_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Prr1_IN_rep2-GSM8445952.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Prt1_ChIP_rep1-GSM8445957/SRR30166601_1.fastq Prt1_ChIP_rep1-GSM8445957/SRR30166601_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Prt1_ChIP_rep1-GSM8445957.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Prt1_ChIP_rep2-GSM8445958/SRR30166600_1.fastq Prt1_ChIP_rep2-GSM8445958/SRR30166600_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Prt1_ChIP_rep2-GSM8445958.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Prt1_IN_rep1-GSM8445955/SRR30166603_1.fastq Prt1_IN_rep1-GSM8445955/SRR30166603_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Prt1_IN_rep1-GSM8445955.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Prt1_IN_rep2-GSM8445956/SRR30166602_1.fastq Prt1_IN_rep2-GSM8445956/SRR30166602_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Prt1_IN_rep2-GSM8445956.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Prz1_ChIP_rep1-GSM8445961/SRR30166597_1.fastq Prz1_ChIP_rep1-GSM8445961/SRR30166597_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Prz1_ChIP_rep1-GSM8445961.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Prz1_ChIP_rep2-GSM8445962/SRR30166596_1.fastq Prz1_ChIP_rep2-GSM8445962/SRR30166596_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Prz1_ChIP_rep2-GSM8445962.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Prz1_IN_rep1-GSM8445959/SRR30166599_1.fastq Prz1_IN_rep1-GSM8445959/SRR30166599_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Prz1_IN_rep1-GSM8445959.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Prz1_IN_rep2-GSM8445960/SRR30166598_1.fastq Prz1_IN_rep2-GSM8445960/SRR30166598_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Prz1_IN_rep2-GSM8445960.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Reb1_ChIP_rep1-GSM8445965/SRR30166673_1.fastq Reb1_ChIP_rep1-GSM8445965/SRR30166673_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Reb1_ChIP_rep1-GSM8445965.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Reb1_ChIP_rep2-GSM8445966/SRR30166672_1.fastq Reb1_ChIP_rep2-GSM8445966/SRR30166672_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Reb1_ChIP_rep2-GSM8445966.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Reb1_IN_rep1-GSM8445963/SRR30166675_1.fastq Reb1_IN_rep1-GSM8445963/SRR30166675_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Reb1_IN_rep1-GSM8445963.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Reb1_IN_rep2-GSM8445964/SRR30166674_1.fastq Reb1_IN_rep2-GSM8445964/SRR30166674_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Reb1_IN_rep2-GSM8445964.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Res1_ChIP_rep1-GSM8445877/SRR30166681_1.fastq Res1_ChIP_rep1-GSM8445877/SRR30166681_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Res1_ChIP_rep1-GSM8445877.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Res1_ChIP_rep2-GSM8445878/SRR30166680_1.fastq Res1_ChIP_rep2-GSM8445878/SRR30166680_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Res1_ChIP_rep2-GSM8445878.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Res1_IN_rep1-GSM8445875/SRR30166683_1.fastq Res1_IN_rep1-GSM8445875/SRR30166683_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Res1_IN_rep1-GSM8445875.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Res1_IN_rep2-GSM8445876/SRR30166682_1.fastq Res1_IN_rep2-GSM8445876/SRR30166682_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Res1_IN_rep2-GSM8445876.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Res2_ChIP_rep1-GSM8445969/SRR30166669_1.fastq Res2_ChIP_rep1-GSM8445969/SRR30166669_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Res2_ChIP_rep1-GSM8445969.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Res2_ChIP_rep2-GSM8445970/SRR30166669_1.fastq Res2_ChIP_rep2-GSM8445970/SRR30166669_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Res2_ChIP_rep2-GSM8445970.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Res2_IN_rep1-GSM8445967/SRR30166671_1.fastq Res2_IN_rep1-GSM8445967/SRR30166671_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Res2_IN_rep1-GSM8445967.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Res2_IN_rep2-GSM8445968/SRR30166670_1.fastq Res2_IN_rep2-GSM8445968/SRR30166670_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Res2_IN_rep2-GSM8445968.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Rst2_ChIP_rep1-GSM8445973/SRR30166666_1.fastq Rst2_ChIP_rep1-GSM8445973/SRR30166666_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Rst2_ChIP_rep1-GSM8445973.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Rst2_ChIP_rep2-GSM8445974/SRR30166665_1.fastq Rst2_ChIP_rep2-GSM8445974/SRR30166665_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Rst2_ChIP_rep2-GSM8445974.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Rst2_IN_rep1-GSM8445971/SRR30166668_1.fastq Rst2_IN_rep1-GSM8445971/SRR30166668_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Rst2_IN_rep1-GSM8445971.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Rst2_IN_rep2-GSM8445972/SRR30166667_1.fastq Rst2_IN_rep2-GSM8445972/SRR30166667_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Rst2_IN_rep2-GSM8445972.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Rsv2_ChIP_rep1-GSM8445977/SRR30166662_1.fastq Rsv2_ChIP_rep1-GSM8445977/SRR30166662_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Rsv2_ChIP_rep1-GSM8445977.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Rsv2_ChIP_rep2-GSM8445978/SRR30166661_1.fastq Rsv2_ChIP_rep2-GSM8445978/SRR30166661_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Rsv2_ChIP_rep2-GSM8445978.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Rsv2_IN_rep1-GSM8445975/SRR30166664_1.fastq Rsv2_IN_rep1-GSM8445975/SRR30166664_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Rsv2_IN_rep1-GSM8445975.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Rsv2_IN_rep2-GSM8445976/SRR30166663_1.fastq Rsv2_IN_rep2-GSM8445976/SRR30166663_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Rsv2_IN_rep2-GSM8445976.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sak1_ChIP_rep1-GSM8445885/SRR30166689_1.fastq Sak1_ChIP_rep1-GSM8445885/SRR30166689_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sak1_ChIP_rep1-GSM8445885.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sak1_ChIP_rep2-GSM8445886/SRR30166688_1.fastq Sak1_ChIP_rep2-GSM8445886/SRR30166688_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sak1_ChIP_rep2-GSM8445886.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sak1_IN_rep1-GSM8445883/SRR30166691_1.fastq Sak1_IN_rep1-GSM8445883/SRR30166691_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sak1_IN_rep1-GSM8445883.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sak1_IN_rep2-GSM8445884/SRR30166690_1.fastq Sak1_IN_rep2-GSM8445884/SRR30166690_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sak1_IN_rep2-GSM8445884.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Scr1_ChIP_rep1-GSM8445981/SRR30166842_1.fastq Scr1_ChIP_rep1-GSM8445981/SRR30166842_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Scr1_ChIP_rep1-GSM8445981.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Scr1_ChIP_rep2-GSM8445982/SRR30166841_1.fastq Scr1_ChIP_rep2-GSM8445982/SRR30166841_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Scr1_ChIP_rep2-GSM8445982.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Scr1_IN_rep1-GSM8445979/SRR30166660_1.fastq Scr1_IN_rep1-GSM8445979/SRR30166660_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Scr1_IN_rep1-GSM8445979.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Scr1_IN_rep2-GSM8445980/SRR30166843_1.fastq Scr1_IN_rep2-GSM8445980/SRR30166843_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Scr1_IN_rep2-GSM8445980.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sep1_ChIP_rep1-GSM8445985/SRR30166838_1.fastq Sep1_ChIP_rep1-GSM8445985/SRR30166838_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sep1_ChIP_rep1-GSM8445985.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sep1_ChIP_rep2-GSM8445986/SRR30166837_1.fastq Sep1_ChIP_rep2-GSM8445986/SRR30166837_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sep1_ChIP_rep2-GSM8445986.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sep1_IN_rep1-GSM8445983/SRR30166840_1.fastq Sep1_IN_rep1-GSM8445983/SRR30166840_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sep1_IN_rep1-GSM8445983.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sep1_IN_rep2-GSM8445984/SRR30166839_1.fastq Sep1_IN_rep2-GSM8445984/SRR30166839_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sep1_IN_rep2-GSM8445984.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sfp1_ChIP_rep1-GSM8445989/SRR30166834_1.fastq Sfp1_ChIP_rep1-GSM8445989/SRR30166834_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sfp1_ChIP_rep1-GSM8445989.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sfp1_ChIP_rep2-GSM8445990/SRR30166833_1.fastq Sfp1_ChIP_rep2-GSM8445990/SRR30166833_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sfp1_ChIP_rep2-GSM8445990.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sfp1_IN_rep1-GSM8445987/SRR30166836_1.fastq Sfp1_IN_rep1-GSM8445987/SRR30166836_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sfp1_IN_rep1-GSM8445987.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sfp1_IN_rep2-GSM8445988/SRR30166835_1.fastq Sfp1_IN_rep2-GSM8445988/SRR30166835_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sfp1_IN_rep2-GSM8445988.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC11D3.11c_ChIP_rep1-GSM8446053/SRR30166585_1.fastq SPAC11D3.11c_ChIP_rep1-GSM8446053/SRR30166585_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC11D3.11c_ChIP_rep1-GSM8446053.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC11D3.11c_ChIP_rep2-GSM8446054/SRR30166584_1.fastq SPAC11D3.11c_ChIP_rep2-GSM8446054/SRR30166584_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC11D3.11c_ChIP_rep2-GSM8446054.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC11D3.11c_IN_rep1-GSM8446051/SRR30166587_1.fastq SPAC11D3.11c_IN_rep1-GSM8446051/SRR30166587_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC11D3.11c_IN_rep1-GSM8446051.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC11D3.11c_IN_rep2-GSM8446052/SRR30166586_1.fastq SPAC11D3.11c_IN_rep2-GSM8446052/SRR30166586_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC11D3.11c_IN_rep2-GSM8446052.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC11D3.17_ChIP_rep1-GSM8446057/SRR30166581_1.fastq SPAC11D3.17_ChIP_rep1-GSM8446057/SRR30166581_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC11D3.17_ChIP_rep1-GSM8446057.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC11D3.17_ChIP_rep2-GSM8446058/SRR30166580_1.fastq SPAC11D3.17_ChIP_rep2-GSM8446058/SRR30166580_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC11D3.17_ChIP_rep2-GSM8446058.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC11D3.17_IN_rep1-GSM8446055/SRR30166583_1.fastq SPAC11D3.17_IN_rep1-GSM8446055/SRR30166583_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC11D3.17_IN_rep1-GSM8446055.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC11D3.17_IN_rep2-GSM8446056/SRR30166582_1.fastq SPAC11D3.17_IN_rep2-GSM8446056/SRR30166582_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC11D3.17_IN_rep2-GSM8446056.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC1327.01c_ChIP_rep1-GSM8446061/SRR30166809_1.fastq SPAC1327.01c_ChIP_rep1-GSM8446061/SRR30166809_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC1327.01c_ChIP_rep1-GSM8446061.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC1327.01c_ChIP_rep2-GSM8446062/SRR30166808_1.fastq SPAC1327.01c_ChIP_rep2-GSM8446062/SRR30166808_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC1327.01c_ChIP_rep2-GSM8446062.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC1327.01c_IN_rep1-GSM8446059/SRR30166811_1.fastq SPAC1327.01c_IN_rep1-GSM8446059/SRR30166811_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC1327.01c_IN_rep1-GSM8446059.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC1327.01c_IN_rep2-GSM8446060/SRR30166810_1.fastq SPAC1327.01c_IN_rep2-GSM8446060/SRR30166810_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC1327.01c_IN_rep2-GSM8446060.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC1F7.11c_ChIP_rep1-GSM8446065/SRR30166805_1.fastq SPAC1F7.11c_ChIP_rep1-GSM8446065/SRR30166805_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC1F7.11c_ChIP_rep1-GSM8446065.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC1F7.11c_ChIP_rep2-GSM8446066/SRR30166804_1.fastq SPAC1F7.11c_ChIP_rep2-GSM8446066/SRR30166804_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC1F7.11c_ChIP_rep2-GSM8446066.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC1F7.11c_IN_rep1-GSM8446063/SRR30166807_1.fastq SPAC1F7.11c_IN_rep1-GSM8446063/SRR30166807_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC1F7.11c_IN_rep1-GSM8446063.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC1F7.11c_IN_rep2-GSM8446064/SRR30166806_1.fastq SPAC1F7.11c_IN_rep2-GSM8446064/SRR30166806_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC1F7.11c_IN_rep2-GSM8446064.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC25B8.11_ChIP_rep1-GSM8446069/SRR30166801_1.fastq SPAC25B8.11_ChIP_rep1-GSM8446069/SRR30166801_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC25B8.11_ChIP_rep1-GSM8446069.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC25B8.11_ChIP_rep2-GSM8446070/SRR30166800_1.fastq SPAC25B8.11_ChIP_rep2-GSM8446070/SRR30166800_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC25B8.11_ChIP_rep2-GSM8446070.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC25B8.11_IN_rep1-GSM8446067/SRR30166803_1.fastq SPAC25B8.11_IN_rep1-GSM8446067/SRR30166803_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC25B8.11_IN_rep1-GSM8446067.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC25B8.11_IN_rep2-GSM8446068/SRR30166802_1.fastq SPAC25B8.11_IN_rep2-GSM8446068/SRR30166802_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC25B8.11_IN_rep2-GSM8446068.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC2H10.01_ChIP_rep1-GSM8446073/SRR30166797_1.fastq SPAC2H10.01_ChIP_rep1-GSM8446073/SRR30166797_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC2H10.01_ChIP_rep1-GSM8446073.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC2H10.01_ChIP_rep2-GSM8446074/SRR30166796_1.fastq SPAC2H10.01_ChIP_rep2-GSM8446074/SRR30166796_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC2H10.01_ChIP_rep2-GSM8446074.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC2H10.01_IN_rep1-GSM8446071/SRR30166799_1.fastq SPAC2H10.01_IN_rep1-GSM8446071/SRR30166799_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC2H10.01_IN_rep1-GSM8446071.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC2H10.01_IN_rep2-GSM8446072/SRR30166798_1.fastq SPAC2H10.01_IN_rep2-GSM8446072/SRR30166798_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC2H10.01_IN_rep2-GSM8446072.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC3C7.04_ChIP_rep1-GSM8446077/SRR30166577_1.fastq SPAC3C7.04_ChIP_rep1-GSM8446077/SRR30166577_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC3C7.04_ChIP_rep1-GSM8446077.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC3C7.04_ChIP_rep2-GSM8446078/SRR30166576_1.fastq SPAC3C7.04_ChIP_rep2-GSM8446078/SRR30166576_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC3C7.04_ChIP_rep2-GSM8446078.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC3C7.04_IN_rep1-GSM8446075/SRR30166579_1.fastq SPAC3C7.04_IN_rep1-GSM8446075/SRR30166579_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC3C7.04_IN_rep1-GSM8446075.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC3C7.04_IN_rep2-GSM8446076/SRR30166578_1.fastq SPAC3C7.04_IN_rep2-GSM8446076/SRR30166578_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC3C7.04_IN_rep2-GSM8446076.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC3F10.12c_ChIP_rep1-GSM8446081/SRR30166573_1.fastq SPAC3F10.12c_ChIP_rep1-GSM8446081/SRR30166573_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC3F10.12c_ChIP_rep1-GSM8446081.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC3F10.12c_ChIP_rep2-GSM8446082/SRR30166572_1.fastq SPAC3F10.12c_ChIP_rep2-GSM8446082/SRR30166572_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC3F10.12c_ChIP_rep2-GSM8446082.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC3F10.12c_IN_rep1-GSM8446079/SRR30166575_1.fastq SPAC3F10.12c_IN_rep1-GSM8446079/SRR30166575_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC3F10.12c_IN_rep1-GSM8446079.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC3F10.12c_IN_rep2-GSM8446080/SRR30166574_1.fastq SPAC3F10.12c_IN_rep2-GSM8446080/SRR30166574_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC3F10.12c_IN_rep2-GSM8446080.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC3H8.08c_ChIP_rep1-GSM8446085/SRR30166569_1.fastq SPAC3H8.08c_ChIP_rep1-GSM8446085/SRR30166569_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC3H8.08c_ChIP_rep1-GSM8446085.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC3H8.08c_ChIP_rep2-GSM8446086/SRR30166568_1.fastq SPAC3H8.08c_ChIP_rep2-GSM8446086/SRR30166568_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC3H8.08c_ChIP_rep2-GSM8446086.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC3H8.08c_IN_rep1-GSM8446083/SRR30166571_1.fastq SPAC3H8.08c_IN_rep1-GSM8446083/SRR30166571_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC3H8.08c_IN_rep1-GSM8446083.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPAC3H8.08c_IN_rep2-GSM8446084/SRR30166570_1.fastq SPAC3H8.08c_IN_rep2-GSM8446084/SRR30166570_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPAC3H8.08c_IN_rep2-GSM8446084.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC16G5.17_ChIP_rep1-GSM8446093/SRR30166761_1.fastq SPBC16G5.17_ChIP_rep1-GSM8446093/SRR30166761_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC16G5.17_ChIP_rep1-GSM8446093.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC16G5.17_ChIP_rep2-GSM8446094/SRR30166760_1.fastq SPBC16G5.17_ChIP_rep2-GSM8446094/SRR30166760_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC16G5.17_ChIP_rep2-GSM8446094.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC16G5.17_IN_rep1-GSM8446091/SRR30166763_1.fastq SPBC16G5.17_IN_rep1-GSM8446091/SRR30166763_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC16G5.17_IN_rep1-GSM8446091.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC16G5.17_IN_rep2-GSM8446092/SRR30166762_1.fastq SPBC16G5.17_IN_rep2-GSM8446092/SRR30166762_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC16G5.17_IN_rep2-GSM8446092.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC1773.12_ChIP_rep1-GSM8446097/SRR30166757_1.fastq SPBC1773.12_ChIP_rep1-GSM8446097/SRR30166757_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC1773.12_ChIP_rep1-GSM8446097.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC1773.12_ChIP_rep2-GSM8446098/SRR30166756_1.fastq SPBC1773.12_ChIP_rep2-GSM8446098/SRR30166756_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC1773.12_ChIP_rep2-GSM8446098.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC1773.12_IN_rep1-GSM8446095/SRR30166759_1.fastq SPBC1773.12_IN_rep1-GSM8446095/SRR30166759_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC1773.12_IN_rep1-GSM8446095.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC1773.12_IN_rep2-GSM8446096/SRR30166758_1.fastq SPBC1773.12_IN_rep2-GSM8446096/SRR30166758_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC1773.12_IN_rep2-GSM8446096.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC1773.16c_ChIP_rep1-GSM8446101/SRR30166753_1.fastq SPBC1773.16c_ChIP_rep1-GSM8446101/SRR30166753_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC1773.16c_ChIP_rep1-GSM8446101.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC1773.16c_ChIP_rep2-GSM8446102/SRR30166752_1.fastq SPBC1773.16c_ChIP_rep2-GSM8446102/SRR30166752_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC1773.16c_ChIP_rep2-GSM8446102.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC1773.16c_IN_rep1-GSM8446099/SRR30166755_1.fastq SPBC1773.16c_IN_rep1-GSM8446099/SRR30166755_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC1773.16c_IN_rep1-GSM8446099.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC1773.16c_IN_rep2-GSM8446100/SRR30166754_1.fastq SPBC1773.16c_IN_rep2-GSM8446100/SRR30166754_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC1773.16c_IN_rep2-GSM8446100.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC530.11c_ChIP_rep1-GSM8446109/SRR30166641_1.fastq SPBC530.11c_ChIP_rep1-GSM8446109/SRR30166641_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC530.11c_ChIP_rep1-GSM8446109.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC530.11c_ChIP_rep2-GSM8446110/SRR30166640_1.fastq SPBC530.11c_ChIP_rep2-GSM8446110/SRR30166640_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC530.11c_ChIP_rep2-GSM8446110.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC530.11c_IN_rep1-GSM8446107/SRR30166643_1.fastq SPBC530.11c_IN_rep1-GSM8446107/SRR30166643_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC530.11c_IN_rep1-GSM8446107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC530.11c_IN_rep2-GSM8446108/SRR30166642_1.fastq SPBC530.11c_IN_rep2-GSM8446108/SRR30166642_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC530.11c_IN_rep2-GSM8446108.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC56F2.05c_ChIP_rep1-GSM8446113/SRR30166637_1.fastq SPBC56F2.05c_ChIP_rep1-GSM8446113/SRR30166637_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC56F2.05c_ChIP_rep1-GSM8446113.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC56F2.05c_ChIP_rep2-GSM8446114/SRR30166636_1.fastq SPBC56F2.05c_ChIP_rep2-GSM8446114/SRR30166636_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC56F2.05c_ChIP_rep2-GSM8446114.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC56F2.05c_IN_rep1-GSM8446111/SRR30166639_1.fastq SPBC56F2.05c_IN_rep1-GSM8446111/SRR30166639_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC56F2.05c_IN_rep1-GSM8446111.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPBC56F2.05c_IN_rep2-GSM8446112/SRR30166638_1.fastq SPBC56F2.05c_IN_rep2-GSM8446112/SRR30166638_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPBC56F2.05c_IN_rep2-GSM8446112.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC18.03_ChIP_rep1-GSM8446117/SRR30166633_1.fastq SPCC18.03_ChIP_rep1-GSM8446117/SRR30166633_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC18.03_ChIP_rep1-GSM8446117.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC18.03_ChIP_rep2-GSM8446118/SRR30166632_1.fastq SPCC18.03_ChIP_rep2-GSM8446118/SRR30166632_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC18.03_ChIP_rep2-GSM8446118.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC18.03_IN_rep1-GSM8446115/SRR30166635_1.fastq SPCC18.03_IN_rep1-GSM8446115/SRR30166635_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC18.03_IN_rep1-GSM8446115.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC18.03_IN_rep2-GSM8446116/SRR30166634_1.fastq SPCC18.03_IN_rep2-GSM8446116/SRR30166634_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC18.03_IN_rep2-GSM8446116.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC320.03_ChIP_rep1-GSM8446121/SRR30166629_1.fastq SPCC320.03_ChIP_rep1-GSM8446121/SRR30166629_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC320.03_ChIP_rep1-GSM8446121.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC320.03_ChIP_rep2-GSM8446122/SRR30166628_1.fastq SPCC320.03_ChIP_rep2-GSM8446122/SRR30166628_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC320.03_ChIP_rep2-GSM8446122.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC320.03_IN_rep1-GSM8446119/SRR30166631_1.fastq SPCC320.03_IN_rep1-GSM8446119/SRR30166631_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC320.03_IN_rep1-GSM8446119.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC320.03_IN_rep2-GSM8446120/SRR30166630_1.fastq SPCC320.03_IN_rep2-GSM8446120/SRR30166630_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC320.03_IN_rep2-GSM8446120.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC417.09c_ChIP_rep1-GSM8446125/SRR30166561_1.fastq SPCC417.09c_ChIP_rep1-GSM8446125/SRR30166561_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC417.09c_ChIP_rep1-GSM8446125.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC417.09c_ChIP_rep2-GSM8446126/SRR30166560_1.fastq SPCC417.09c_ChIP_rep2-GSM8446126/SRR30166560_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC417.09c_ChIP_rep2-GSM8446126.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC417.09c_IN_rep1-GSM8446123/SRR30166563_1.fastq SPCC417.09c_IN_rep1-GSM8446123/SRR30166563_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC417.09c_IN_rep1-GSM8446123.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC417.09c_IN_rep2-GSM8446124/SRR30166562_1.fastq SPCC417.09c_IN_rep2-GSM8446124/SRR30166562_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC417.09c_IN_rep2-GSM8446124.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC757.04_ChIP_rep1-GSM8446129/SRR30166557_1.fastq SPCC757.04_ChIP_rep1-GSM8446129/SRR30166557_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC757.04_ChIP_rep1-GSM8446129.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC757.04_ChIP_rep2-GSM8446130/SRR30166556_1.fastq SPCC757.04_ChIP_rep2-GSM8446130/SRR30166556_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC757.04_ChIP_rep2-GSM8446130.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC757.04_IN_rep1-GSM8446127/SRR30166559_1.fastq SPCC757.04_IN_rep1-GSM8446127/SRR30166559_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC757.04_IN_rep1-GSM8446127.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC757.04_IN_rep2-GSM8446128/SRR30166558_1.fastq SPCC757.04_IN_rep2-GSM8446128/SRR30166558_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC757.04_IN_rep2-GSM8446128.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC777.02_ChIP_rep1-GSM8446133/SRR30166553_1.fastq SPCC777.02_ChIP_rep1-GSM8446133/SRR30166553_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC777.02_ChIP_rep1-GSM8446133.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC777.02_ChIP_rep2-GSM8446134/SRR30166552_1.fastq SPCC777.02_ChIP_rep2-GSM8446134/SRR30166552_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC777.02_ChIP_rep2-GSM8446134.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC777.02_IN_rep1-GSM8446131/SRR30166555_1.fastq SPCC777.02_IN_rep1-GSM8446131/SRR30166555_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC777.02_IN_rep1-GSM8446131.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC777.02_IN_rep2-GSM8446132/SRR30166554_1.fastq SPCC777.02_IN_rep2-GSM8446132/SRR30166554_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC777.02_IN_rep2-GSM8446132.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC965.10_ChIP_rep1-GSM8446137/SRR30166893_1.fastq SPCC965.10_ChIP_rep1-GSM8446137/SRR30166893_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC965.10_ChIP_rep1-GSM8446137.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC965.10_ChIP_rep2-GSM8446138/SRR30166892_1.fastq SPCC965.10_ChIP_rep2-GSM8446138/SRR30166892_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC965.10_ChIP_rep2-GSM8446138.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC965.10_IN_rep1-GSM8446135/SRR30166895_1.fastq SPCC965.10_IN_rep1-GSM8446135/SRR30166895_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC965.10_IN_rep1-GSM8446135.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py SPCC965.10_IN_rep2-GSM8446136/SRR30166894_1.fastq SPCC965.10_IN_rep2-GSM8446136/SRR30166894_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPCC965.10_IN_rep2-GSM8446136.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sre1_ChIP_rep1-GSM8446009/SRR30166766_1.fastq Sre1_ChIP_rep1-GSM8446009/SRR30166766_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sre1_ChIP_rep1-GSM8446009.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sre1_ChIP_rep2-GSM8446010/SRR30166765_1.fastq Sre1_ChIP_rep2-GSM8446010/SRR30166765_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sre1_ChIP_rep2-GSM8446010.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sre1_IN_rep1-GSM8446007/SRR30166768_1.fastq Sre1_IN_rep1-GSM8446007/SRR30166768_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sre1_IN_rep1-GSM8446007.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Sre1_IN_rep2-GSM8446008/SRR30166767_1.fastq Sre1_IN_rep2-GSM8446008/SRR30166767_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Sre1_IN_rep2-GSM8446008.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Stb3_ChIP_rep1-GSM8446013/SRR30166658_1.fastq Stb3_ChIP_rep1-GSM8446013/SRR30166658_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Stb3_ChIP_rep1-GSM8446013.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Stb3_ChIP_rep2-GSM8446014/SRR30166657_1.fastq Stb3_ChIP_rep2-GSM8446014/SRR30166657_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Stb3_ChIP_rep2-GSM8446014.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Stb3_IN_rep1-GSM8446011/SRR30166764_1.fastq Stb3_IN_rep1-GSM8446011/SRR30166764_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Stb3_IN_rep1-GSM8446011.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Stb3_IN_rep2-GSM8446012/SRR30166659_1.fastq Stb3_IN_rep2-GSM8446012/SRR30166659_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Stb3_IN_rep2-GSM8446012.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ste11_ChIP_rep1-GSM8446017/SRR30166654_1.fastq Ste11_ChIP_rep1-GSM8446017/SRR30166654_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ste11_ChIP_rep1-GSM8446017.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ste11_ChIP_rep2-GSM8446018/SRR30166653_1.fastq Ste11_ChIP_rep2-GSM8446018/SRR30166653_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ste11_ChIP_rep2-GSM8446018.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ste11_IN_rep1-GSM8446015/SRR30166656_1.fastq Ste11_IN_rep1-GSM8446015/SRR30166656_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ste11_IN_rep1-GSM8446015.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Ste11_IN_rep2-GSM8446016/SRR30166655_1.fastq Ste11_IN_rep2-GSM8446016/SRR30166655_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ste11_IN_rep2-GSM8446016.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Teb1_ChIP_rep1-GSM8445889/SRR30166685_1.fastq Teb1_ChIP_rep1-GSM8445889/SRR30166685_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Teb1_ChIP_rep1-GSM8445889.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Teb1_ChIP_rep2-GSM8445890/SRR30166684_1.fastq Teb1_ChIP_rep2-GSM8445890/SRR30166684_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Teb1_ChIP_rep2-GSM8445890.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Teb1_IN_rep1-GSM8445887/SRR30166687_1.fastq Teb1_IN_rep1-GSM8445887/SRR30166687_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Teb1_IN_rep1-GSM8445887.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Teb1_IN_rep2-GSM8445888/SRR30166686_1.fastq Teb1_IN_rep2-GSM8445888/SRR30166686_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Teb1_IN_rep2-GSM8445888.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Thi1_ChIP_rep1-GSM8446021/SRR30166649_1.fastq Thi1_ChIP_rep1-GSM8446021/SRR30166649_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Thi1_ChIP_rep1-GSM8446021.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Thi1_ChIP_rep2-GSM8446022/SRR30166648_1.fastq Thi1_ChIP_rep2-GSM8446022/SRR30166648_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Thi1_ChIP_rep2-GSM8446022.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Thi1_IN_rep1-GSM8446019/SRR30166652_1.fastq Thi1_IN_rep1-GSM8446019/SRR30166652_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Thi1_IN_rep1-GSM8446019.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Thi1_IN_rep2-GSM8446020/SRR30166650_1.fastq Thi1_IN_rep2-GSM8446020/SRR30166650_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Thi1_IN_rep2-GSM8446020.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Thi5_ChIP_rep1-GSM8446025/SRR30166645_1.fastq Thi5_ChIP_rep1-GSM8446025/SRR30166645_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Thi5_ChIP_rep1-GSM8446025.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Thi5_ChIP_rep2-GSM8446026/SRR30166644_1.fastq Thi5_ChIP_rep2-GSM8446026/SRR30166644_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Thi5_ChIP_rep2-GSM8446026.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Thi5_IN_rep1-GSM8446023/SRR30166647_1.fastq Thi5_IN_rep1-GSM8446023/SRR30166647_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Thi5_IN_rep1-GSM8446023.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Thi5_IN_rep2-GSM8446024/SRR30166646_1.fastq Thi5_IN_rep2-GSM8446024/SRR30166646_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Thi5_IN_rep2-GSM8446024.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe1_ChIP_rep1-GSM8446029/SRR30166825_1.fastq Toe1_ChIP_rep1-GSM8446029/SRR30166825_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe1_ChIP_rep1-GSM8446029.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe1_ChIP_rep2-GSM8446030/SRR30166824_1.fastq Toe1_ChIP_rep2-GSM8446030/SRR30166824_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe1_ChIP_rep2-GSM8446030.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe1_IN_rep1-GSM8446027/SRR30166827_1.fastq Toe1_IN_rep1-GSM8446027/SRR30166827_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe1_IN_rep1-GSM8446027.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe1_IN_rep2-GSM8446028/SRR30166826_1.fastq Toe1_IN_rep2-GSM8446028/SRR30166826_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe1_IN_rep2-GSM8446028.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe2_ChIP_rep1-GSM8446033/SRR30166821_1.fastq Toe2_ChIP_rep1-GSM8446033/SRR30166821_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe2_ChIP_rep1-GSM8446033.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe2_ChIP_rep2-GSM8446034/SRR30166820_1.fastq Toe2_ChIP_rep2-GSM8446034/SRR30166820_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe2_ChIP_rep2-GSM8446034.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe2_IN_rep1-GSM8446031/SRR30166823_1.fastq Toe2_IN_rep1-GSM8446031/SRR30166823_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe2_IN_rep1-GSM8446031.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe2_IN_rep2-GSM8446032/SRR30166822_1.fastq Toe2_IN_rep2-GSM8446032/SRR30166822_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe2_IN_rep2-GSM8446032.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe3_ChIP_rep1-GSM8446037/SRR30166817_1.fastq Toe3_ChIP_rep1-GSM8446037/SRR30166817_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe3_ChIP_rep1-GSM8446037.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe3_ChIP_rep2-GSM8446038/SRR30166816_1.fastq Toe3_ChIP_rep2-GSM8446038/SRR30166816_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe3_ChIP_rep2-GSM8446038.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe3_IN_rep1-GSM8446035/SRR30166819_1.fastq Toe3_IN_rep1-GSM8446035/SRR30166819_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe3_IN_rep1-GSM8446035.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe3_IN_rep2-GSM8446036/SRR30166818_1.fastq Toe3_IN_rep2-GSM8446036/SRR30166818_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe3_IN_rep2-GSM8446036.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe4_ChIP_rep1-GSM8446041/SRR30166813_1.fastq Toe4_ChIP_rep1-GSM8446041/SRR30166813_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe4_ChIP_rep1-GSM8446041.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe4_ChIP_rep2-GSM8446042/SRR30166812_1.fastq Toe4_ChIP_rep2-GSM8446042/SRR30166812_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe4_ChIP_rep2-GSM8446042.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe4_IN_rep1-GSM8446039/SRR30166815_1.fastq Toe4_IN_rep1-GSM8446039/SRR30166815_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe4_IN_rep1-GSM8446039.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Toe4_IN_rep2-GSM8446040/SRR30166814_1.fastq Toe4_IN_rep2-GSM8446040/SRR30166814_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Toe4_IN_rep2-GSM8446040.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Untagged_ChIP_rep1-GSM8446141/SRR30166745_1.fastq Untagged_ChIP_rep1-GSM8446141/SRR30166745_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Untagged_ChIP_rep1-GSM8446141.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Untagged_ChIP_rep2-GSM8446142/SRR30166744_1.fastq Untagged_ChIP_rep2-GSM8446142/SRR30166744_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Untagged_ChIP_rep2-GSM8446142.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Untagged_IN_rep1-GSM8446139/SRR30166747_1.fastq Untagged_IN_rep1-GSM8446139/SRR30166747_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Untagged_IN_rep1-GSM8446139.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Untagged_IN_rep2-GSM8446140/SRR30166746_1.fastq Untagged_IN_rep2-GSM8446140/SRR30166746_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Untagged_IN_rep2-GSM8446140.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Zas1_ChIP_rep1-GSM8445893/SRR30166681_1.fastq Zas1_ChIP_rep1-GSM8445893/SRR30166681_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Zas1_ChIP_rep1-GSM8445893.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Zas1_ChIP_rep2-GSM8445894/SRR30166680_1.fastq Zas1_ChIP_rep2-GSM8445894/SRR30166680_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Zas1_ChIP_rep2-GSM8445894.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Zas1_IN_rep1-GSM8445891/SRR30166683_1.fastq Zas1_IN_rep1-GSM8445891/SRR30166683_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Zas1_IN_rep1-GSM8445891.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Zas1_IN_rep2-GSM8445892/SRR30166682_1.fastq Zas1_IN_rep2-GSM8445892/SRR30166682_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Zas1_IN_rep2-GSM8445892.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Zip1_ChIP_rep1-GSM8446045/SRR30166593_1.fastq Zip1_ChIP_rep1-GSM8446045/SRR30166593_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Zip1_ChIP_rep1-GSM8446045.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Zip1_ChIP_rep2-GSM8446046/SRR30166592_1.fastq Zip1_ChIP_rep2-GSM8446046/SRR30166592_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Zip1_ChIP_rep2-GSM8446046.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Zip1_IN_rep1-GSM8446043/SRR30166595_1.fastq Zip1_IN_rep1-GSM8446043/SRR30166595_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Zip1_IN_rep1-GSM8446043.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a
python ~/code/PEFastqToTabDelimited.py Zip1_IN_rep2-GSM8446044/SRR30166594_1.fastq Zip1_IN_rep2-GSM8446044/SRR30166594_2.fastq -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2 -p 20 -v 2 -a -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/Fungi/Schizosaccharomyces_pombe.ASM294v2/bowtie-indexes/Schizosaccharomyces_pombe.ASM294v2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Zip1_IN_rep2-GSM8446044.2x36mers.Schizosaccharomyces_pombe.ASM294v2.a