cd /N/dc2/projects/marinovg/2015-11-20-Paramecium-MNAse; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF957-A-5H-22_S41_R1_001.fastq.36mers.bz2 GSF957-A-5H-22_S41_R2_001.fastq.36mers.bz2 /N/dc2/projects/marinovg/2015-06-17-ATAC-seq-data/L0007-Lynch-Georgi-Tetra-707_S98-M01529-L001_R2_001.36mers.bz2 | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - L22-Paramecium_tetraurelia-MNAse-15min-65C-12cycles.2x36mers.unique
cd /N/dc2/projects/marinovg/2015-11-20-Paramecium-MNAse; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF957-A-5A-23_S42_R1_001.fastq.36mers.bz2 GSF957-A-5A-23_S42_R2_001.fastq.36mers.bz2 /N/dc2/projects/marinovg/2015-06-17-ATAC-seq-data/L0007-Lynch-Georgi-Tetra-707_S98-M01529-L001_R2_001.36mers.bz2 | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - L23-Paramecium_tetraurelia-MNAse-15min-60C-0.5NaCl-12cycles.2x36mers.unique
cd /N/dc2/projects/marinovg/2015-11-20-Paramecium-MNAse; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF957-A-5B-24_S43_R1_001.fastq.36mers.bz2 GSF957-A-5B-24_S43_R2_001.fastq.36mers.bz2 /N/dc2/projects/marinovg/2015-06-17-ATAC-seq-data/L0007-Lynch-Georgi-Tetra-707_S98-M01529-L001_R2_001.36mers.bz2 | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - L24-Paramecium_tetraurelia-MNAse-15min-45C-0.5NaCl-12cycles.2x36mers.unique