cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/BAMtoFASTQ.py /N/dc2/projects/marinovg/GeorgiLibrariesSequencing/L0039-Tetrahymena_thermophila-ChIP-Input_65C/L39-Tetrahymena_thermophila-Input_65C.2x36mers.unique.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.chrom.sizes - -ignoreChromSizes -OneEndOnly 1 | gzip >  L39-Tetrahymena_thermophila-Input_65C.2x36mers.end1.fastq.gz
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/BAMtoFASTQ.py /N/dc2/projects/marinovg/GeorgiLibrariesSequencing/L0040-Tetrahymena_thermophila-ChIP-Input_65C_0.5N_NaCl/L40-Tetrahymena_thermophila-Input_65C_0.5N_NaCl.2x36mers.unique.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.chrom.sizes - -ignoreChromSizes -OneEndOnly 1 | gzip >  L40-Tetrahymena_thermophila-Input_65C_0.5N_NaCl.2x36mers.end1.fastq.gz
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/BAMtoFASTQ.py /N/dc2/projects/marinovg/GeorgiLibrariesSequencing/L0041-Tetrahymena_thermophila-ChIP-Input_60C_0.5N_NaCl/L41-Tetrahymena_thermophila-Input_60C_0.5N_NaCl.2x36mers.unique.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.chrom.sizes - -ignoreChromSizes -OneEndOnly 1 | gzip >  L41-Tetrahymena_thermophila-Input_60C_0.5N_NaCl.2x36mers.end1.fastq.gz
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/BAMtoFASTQ.py /N/dc2/projects/marinovg/GeorgiLibrariesSequencing/L0042-Tetrahymena_thermophila-ChIP-Input_45C_0.5N_NaCl/L42-Tetrahymena_thermophila-Input_45C_0.5N_NaCl.2x36mers.unique.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.chrom.sizes - -ignoreChromSizes -OneEndOnly 1 | gzip >  L42-Tetrahymena_thermophila-Input_45C_0.5N_NaCl.2x36mers.end1.fastq.gz
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/BAMtoFASTQ.py /N/dc2/projects/marinovg/GeorgiLibrariesSequencing/L0043-Tetrahymena_thermophila-ChIP-H3K4me3/L43-Tetrahymena_thermophila-H3K4me3.2x36mers.unique.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.chrom.sizes - -ignoreChromSizes -OneEndOnly 1 | gzip >  L43-Tetrahymena_thermophila-H3K4me3.2x36mers.end1.fastq.gz
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/BAMtoFASTQ.py /N/dc2/projects/marinovg/GeorgiLibrariesSequencing/L0044-Tetrahymena_thermophila-ChIP-H3K27ac/L44-Tetrahymena_thermophila-H3K27ac.2x36mers.unique.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.chrom.sizes - -ignoreChromSizes -OneEndOnly 1 | gzip >  L44-Tetrahymena_thermophila-H3K27ac.2x36mers.end1.fastq.gz
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/BAMtoFASTQ.py /N/dc2/projects/marinovg/GeorgiLibrariesSequencing/L0039-Tetrahymena_thermophila-ChIP-Input_65C/L39-Tetrahymena_thermophila-Input_65C.2x36mers.unique.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.chrom.sizes - -ignoreChromSizes -OneEndOnly 2 | gzip >  L39-Tetrahymena_thermophila-Input_65C.2x36mers.end2.fastq.gz
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/BAMtoFASTQ.py /N/dc2/projects/marinovg/GeorgiLibrariesSequencing/L0040-Tetrahymena_thermophila-ChIP-Input_65C_0.5N_NaCl/L40-Tetrahymena_thermophila-Input_65C_0.5N_NaCl.2x36mers.unique.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.chrom.sizes - -ignoreChromSizes -OneEndOnly 2 | gzip >  L40-Tetrahymena_thermophila-Input_65C_0.5N_NaCl.2x36mers.end2.fastq.gz
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/BAMtoFASTQ.py /N/dc2/projects/marinovg/GeorgiLibrariesSequencing/L0041-Tetrahymena_thermophila-ChIP-Input_60C_0.5N_NaCl/L41-Tetrahymena_thermophila-Input_60C_0.5N_NaCl.2x36mers.unique.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.chrom.sizes - -ignoreChromSizes -OneEndOnly 2 | gzip >  L41-Tetrahymena_thermophila-Input_60C_0.5N_NaCl.2x36mers.end2.fastq.gz
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/BAMtoFASTQ.py /N/dc2/projects/marinovg/GeorgiLibrariesSequencing/L0042-Tetrahymena_thermophila-ChIP-Input_45C_0.5N_NaCl/L42-Tetrahymena_thermophila-Input_45C_0.5N_NaCl.2x36mers.unique.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.chrom.sizes - -ignoreChromSizes -OneEndOnly 2 | gzip >  L42-Tetrahymena_thermophila-Input_45C_0.5N_NaCl.2x36mers.end2.fastq.gz
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/BAMtoFASTQ.py /N/dc2/projects/marinovg/GeorgiLibrariesSequencing/L0043-Tetrahymena_thermophila-ChIP-H3K4me3/L43-Tetrahymena_thermophila-H3K4me3.2x36mers.unique.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.chrom.sizes - -ignoreChromSizes -OneEndOnly 2 | gzip >  L43-Tetrahymena_thermophila-H3K4me3.2x36mers.end2.fastq.gz
cd /N/dc2/projects/marinovg/2016-01-22-Tetrahymena-H3K4me3-H3K27ac-additional-reads; python /N/dc2/projects/marinovg/code/BAMtoFASTQ.py /N/dc2/projects/marinovg/GeorgiLibrariesSequencing/L0044-Tetrahymena_thermophila-ChIP-H3K27ac/L44-Tetrahymena_thermophila-H3K27ac.2x36mers.unique.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20+chrM.chrom.sizes - -ignoreChromSizes -OneEndOnly 2 | gzip >  L44-Tetrahymena_thermophila-H3K27ac.2x36mers.end2.fastq.gz