cd /N/dc2/projects/marinovg/2015-11-20-Tetrahymena-H3K4me3-H3K27ac; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF957-A-L39_S46_R1_001.fastq.36mers.bz2 GSF957-A-L39_S46_R2_001.fastq.36mers.bz2 | /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/2015-11-20-Tetrahymena-H3K4me3-H3K27ac; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF957-A-L40_S47_R1_001.fastq.36mers.bz2 GSF957-A-L40_S47_R2_001.fastq.36mers.bz2 | /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/2015-11-20-Tetrahymena-H3K4me3-H3K27ac; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF957-A-L41_S39_R1_001.fastq.36mers.bz2 GSF957-A-L41_S39_R2_001.fastq.36mers.bz2 | /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 - L41-Tetrahymena_thermophila-Input_60C_0.5N_NaCl.2x36mers.unique
cd /N/dc2/projects/marinovg/2015-11-20-Tetrahymena-H3K4me3-H3K27ac; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF957-A-L42_S40_R1_001.fastq.36mers.bz2 GSF957-A-L42_S40_R2_001.fastq.36mers.bz2 | /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/2015-11-20-Tetrahymena-H3K4me3-H3K27ac; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF957-A-L43_S45_R1_001.fastq.36mers.bz2 GSF957-A-L43_S45_R2_001.fastq.36mers.bz2 | /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 - L43-Tetrahymena_thermophila-H3K4me3.2x36mers.unique
cd /N/dc2/projects/marinovg/2015-11-20-Tetrahymena-H3K4me3-H3K27ac; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF957-A-L44_S44_R1_001.fastq.36mers.bz2 GSF957-A-L44_S44_R2_001.fastq.36mers.bz2 | /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/2015-11-20-Tetrahymena-H3K4me3-H3K27ac; bzip2 -cd GSF957-A-L39_S46_R1_001.fastq.36mers.bz2 | /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/2015-11-20-Tetrahymena-H3K4me3-H3K27ac; bzip2 -cd GSF957-A-L40_S47_R1_001.fastq.36mers.bz2 | /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/2015-11-20-Tetrahymena-H3K4me3-H3K27ac; bzip2 -cd GSF957-A-L41_S39_R1_001.fastq.36mers.bz2 | /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 - L41-Tetrahymena_thermophila-Input_60C_0.5N_NaCl.36mers.unique
cd /N/dc2/projects/marinovg/2015-11-20-Tetrahymena-H3K4me3-H3K27ac; bzip2 -cd GSF957-A-L42_S40_R1_001.fastq.36mers.bz2 | /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/2015-11-20-Tetrahymena-H3K4me3-H3K27ac; bzip2 -cd GSF957-A-L43_S45_R1_001.fastq.36mers.bz2 | /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 - L43-Tetrahymena_thermophila-H3K4me3.36mers.unique
cd /N/dc2/projects/marinovg/2015-11-20-Tetrahymena-H3K4me3-H3K27ac; bzip2 -cd GSF957-A-L44_S44_R1_001.fastq.36mers.bz2 | /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