cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF957-A-L39_S32_R1_001.36mers.fastq.gz,L39-Tetrahymena_thermophila-Input_65C.2x36mers.end1.sorted.fastq.gz	GSF957-A-L39_S32_R2_001.36mers.fastq.gz,L39-Tetrahymena_thermophila-Input_65C.2x36mers.end2.sorted.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.fa - | samtools sort - L39-Tetrahymena_thermophila-Input_65C.2x36mers.unique
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF957-A-L40_S33_R1_001.36mers.fastq.gz,L40-Tetrahymena_thermophila-Input_65C_0.5N_NaCl.2x36mers.end1.sorted.fastq.gz GSF957-A-L40_S33_R2_001.36mers.fastq.gz,L40-Tetrahymena_thermophila-Input_65C_0.5N_NaCl.2x36mers.end2.sorted.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.fa - | samtools sort - L40-Tetrahymena_thermophila-Input_65C_0.5N_NaCl.2x36mers.unique
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF957-A-L42_S35_R1_001.36mers.fastq.gz,L42-Tetrahymena_thermophila-Input_45C_0.5N_NaCl.2x36mers.end1.sorted.fastq.gz GSF957-A-L42_S35_R2_001.36mers.fastq.gz,L42-Tetrahymena_thermophila-Input_45C_0.5N_NaCl.2x36mers.end2.sorted.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.fa - | samtools sort - L42-Tetrahymena_thermophila-Input_45C_0.5N_NaCl.2x36mers.unique
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF957-A-L44_S37_R1_001.36mers.fastq.gz,L44-Tetrahymena_thermophila-H3K27ac.2x36mers.end1.sorted.fastq.gz GSF957-A-L44_S37_R2_001.36mers.fastq.gz,L44-Tetrahymena_thermophila-H3K27ac.2x36mers.end2.sorted.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.fa - | samtools sort - L44-Tetrahymena_thermophila-H3K27ac.2x36mers.unique
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; zcat GSF957-A-L39_S32_R1_001.36mers.fastq.gz L39-Tetrahymena_thermophila-Input_65C.2x36mers.end1.sorted.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.fa - | samtools sort - L39-Tetrahymena_thermophila-Input_65C.36mers.unique
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; zcat GSF957-A-L40_S33_R1_001.36mers.fastq.gz L40-Tetrahymena_thermophila-Input_65C_0.5N_NaCl.2x36mers.end1.sorted.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.fa - | samtools sort - L40-Tetrahymena_thermophila-Input_65C_0.5N_NaCl.36mers.unique
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; zcat GSF957-A-L42_S35_R1_001.36mers.fastq.gz L42-Tetrahymena_thermophila-Input_45C_0.5N_NaCl.2x36mers.end1.sorted.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.fa - | samtools sort - L42-Tetrahymena_thermophila-Input_45C_0.5N_NaCl.36mers.unique
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; zcat GSF957-A-L44_S37_R1_001.36mers.fastq.gz L44-Tetrahymena_thermophila-H3K27ac.2x36mers.end1.sorted.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.fa - | samtools sort - L44-Tetrahymena_thermophila-H3K27ac.36mers.unique