python ~/code/PEFastqToTabDelimited.py L374-fixed_ATAC_45C_1M.end1.fastq.gz L374-fixed_ATAC_45C_1M.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | ~/programs/samtools-0.1.18/samtools sort - L374-fixed_ATAC_45C_1M.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L375-fixed_ATAC_45C_10M.end1.fastq.gz L375-fixed_ATAC_45C_10M.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | ~/programs/samtools-0.1.18/samtools sort - L375-fixed_ATAC_45C_10M.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L376-fixed_ATAC_stationary_1M.end1.fastq.gz L376-fixed_ATAC_stationary_1M.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | ~/programs/samtools-0.1.18/samtools sort - L376-fixed_ATAC_stationary_1M.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L377-fixed_ATAC_stationary_10M.end1.fastq.gz L377-fixed_ATAC_stationary_10M.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bowtie-indexes/all.fa - | ~/programs/samtools-0.1.18/samtools sort - L377-fixed_ATAC_stationary_10M.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L464-Diamide-0_min-rep1.end1.fastq.gz L464-Diamide-0_min-rep1.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L464-Diamide-0_min-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L465-Diamide-0_min-rep2.end1.fastq.gz L465-Diamide-0_min-rep2.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L465-Diamide-0_min-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L466-Diamide-15_min-rep1.end1.fastq.gz L466-Diamide-15_min-rep1.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L466-Diamide-15_min-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L467-Diamide-15_min-rep2.end1.fastq.gz L467-Diamide-15_min-rep2.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L467-Diamide-15_min-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L468-Diamide-30_min-rep1.end1.fastq.gz L468-Diamide-30_min-rep1.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L468-Diamide-30_min-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L469-Diamide-30_min-rep2.end1.fastq.gz L469-Diamide-30_min-rep2.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L469-Diamide-30_min-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L470-Diamide-45_min-rep1.end1.fastq.gz L470-Diamide-45_min-rep1.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L470-Diamide-45_min-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L471-Diamide-45_min-rep2.end1.fastq.gz L471-Diamide-45_min-rep2.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L471-Diamide-45_min-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L472-Diamide-60_min-rep1.end1.fastq.gz L472-Diamide-60_min-rep1.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L472-Diamide-60_min-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L473-Diamide-60_min-rep2.end1.fastq.gz L473-Diamide-60_min-rep2.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L473-Diamide-60_min-rep2.2x36mers.unique